classified
Nandini Badarinarayan
James Malone
Helen Parkinson
0.4
http://bioconductor.org/packages/2.4/bioc/html/annaffy.html
This package functions for handling data from Bioconductor Affymetrix annotation data packages.Allows searching biological metadata using various criteria.
'annaffy'
Nandini Badarinarayan
Nandini Badarinarayan
'flowUtils'
This package provides utilities for flow cytometry data.
http://bioconductor.org/packages/2.4/bioc/html/flowUtils.html
http://www.rubion.rub.de/labor/pdf/BASREAD.pdf
This program may be used to read out image data from all scanners of the FujiFilm BAS series (BAS1000, BAS1500, BAS1800, BAS2000, BAS2500, BAS3000, BAS5000) and the FujiFilm FLA scanners (FLA-2000, FLA-3000).
BasReader 3.01
Nandini Badarinarayan
average log expression across arrays (ALE)
arrayWoRx 2.0
Nandini Badarinarayan
http://www.chem.agilent.com/
Scan Control Application software
Scan Control Software is the user interface software that controls the Agilent scanner. This software is usable only with the Agilent high-resolution scanner (G2565CA) or high-resolution scanner upgrade. It will not function with earlier scanner versions
Agilent Scan Control
Nandini Badarinarayan
Nandini Badarinarayan
A Graphical User Interface for the limma Microarray package
limmaGUI
http://bioconductor.org/packages/2.4/bioc/html/limmaGUI.html
Nandini Badarinarayan
Multivariate correlation estimation and statistical inference.
'CORREP'
http://bioconductor.org/packages/2.4/bioc/html/CORREP.html
'exonmap'
http://bioconductor.org/packages/2.4/bioc/html/exonmap.html
This package provides fine grained annotation of Affymetrix exon arrays, including mappings between the array probes and probesets and the Ensembl exons, transcripts and genes they target.
Nandini Badarinarayan
Illumina
rank product non-parametric method
pamr
http://bioconductor.org/packages/2.4/bioc/html/pamr.html
Nandini Badarinarayan
Some functions for sample classification in microarrays
http://bioconductor.org/packages/2.4/bioc/html/MEDME.html
MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments
MEDME
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/PAnnBuilder.html
Processing annotation data from public data repositories and building annoation data packages.
PAnnBuilder
Nandini Badarinarayan
ANNOVA
'ANOVA'
http://www.bioconductor.org/packages/2.3/bioc/html/gcrma.html
Background adjustment using sequence information
gcRMA quantification
Nandini Badarinarayan
webbioc
An integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users.
http://bioconductor.org/packages/2.4/bioc/html/webbioc.html
Nandini Badarinarayan
software
OBI
James Malone
Helen Parkinson
Software is a series of encoded instructions that can be directly executed by a processing unit or transformed in to a form that can be. For programming texts that are syntactically correct and which are in a language that can be executed by an interpreter this would correspond to the tokenized version of the text stripped of comments.
Software is a specification which is a series of encoded instructions that can be directly executed by a processing unit or transformed in to a form that can be. For programming texts that are syntactically correct and which are in a language that can be executed by an interpreter this would correspond to the tokenized version of the text stripped of comments.
http://purl.obolibrary.org/obo/IAO_0000010
Tomasz Adamusiak
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/biomaRt.html
The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries.
'biomaRT'
Nandini Badarinarayan
gpr format
2-sample pooled t-test
http://bioconductor.org/packages/2.4/bioc/html/convert.html
Define coerce methods for microarray data objects.
'convert'
Nandini Badarinarayan
The AffyCompatible package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. The package also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files.
http://bioconductor.org/packages/2.4/bioc/html/AffyCompatible.html
'AffyCompatible'
Nandini Badarinarayan
ARACNE algorithm
http://bioconductor.org/packages/2.4/bioc/html/BicARE.html
This package is dedicated to biclustering analysis which allows to discover sets of genes that have the same expression pattern accross a set of samples
'BicARE'
Nandini Badarinarayan
ScISI
http://bioconductor.org/packages/2.4/bioc/html/ScISI.html
Package to create In Silico Interactomes
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/affyContam.html
affyContam functions for structured corruption of cel file data to demonstrate QA effectiveness
'affyContam'
Nandini Badarinarayan
Category analysis
Iteratively ReWeighted Least Squares
http://bioconductor.org/packages/2.4/bioc/html/RLMM.html
Nandini Badarinarayan
RLMM
A Genotype Calling Algorithm for Affymetrix SNP Arrays
Nandini Badarinarayan
gpls
Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification.
http://bioconductor.org/packages/2.4/bioc/html/gpls.html
Empirical Bayes rule
gff_format
TIBCO Software Inc
Nandini Badarinarayan
minet
http://bioconductor.org/packages/2.4/bioc/html/minet.html
This package implements various algorithms for inferring mutual information networks from data. All the algorithms compute the mutual information matrix in order to infer a network. Several mutual information estimators are implemented.
Rosetta Biosoftware
A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data.
PERSON: James Malone
PERSON: Elisabetta Manduchi
class prediction objective
http://bioconductor.org/packages/2.4/bioc/html/sizepower.html
Nandini Badarinarayan
This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study. The user is referred to the cited references for technical background on the methodology underpinning these calculations. This package provides support for five types of sample size and power calculations.
sizepower
http://www.bahlerlab.info/resources/
These scripts are for primer design and initial microarray data processing and are available as .zip files:
Initial microarray data processing (data filtering, local normalisation and quality control)
Nandini Badarinarayan
RMA++
The ANCOVA global test is a test for the association between expression values and clinical entities. The test is carried out by comparison of linear models via the extra sum of squares principle. If the mean expression level for at least one gene diers between corresponding models the global null hypothesis, which is the intersection of all single gene null hypotheses, is violated. FDR
ANCOVA
Expression Console™ software supports probe set summarization and CHP file generation for 3' expression (e.g., GeneChip® Human Genome U133 Plus 2.0 Array), gene-level (e.g., GeneChip® Human Gene 1.0 ST array) and exon-level arrays (e.g., GeneChip® Human Exon 1.0 ST Array). The Expression Console workflow provides the user with a choice of the more commonly used probe set summarization algorithms
Affymetrix Expression Console
Nandini Badarinarayan
http://www.affymetrix.com/
'cls'
Lognormal Normal Model
http://bioconductor.org/packages/2.4/bioc/html/GenomeGraphs.html
Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system.
GenomeGraphs
Nandini Badarinarayan
'beadarraySNP'
Importing data from Illumina SNP experiments and performing copy number calculations and reports.
http://bioconductor.org/packages/2.4/bioc/html/beadarraySNP.html
Nandini Badarinarayan
multiple testing which includes controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included.
Multiple testing
SBML model
ChipSkipper V0.99
Nandini Badarinarayan
The package contains functions for pre-processing Affymetrix data using the RMA+ and the RMA++ methods.
RefPlus
http://bioconductor.org/packages/2.4/bioc/html/RefPlus.html
Nandini Badarinarayan
Nandini Badarinarayan
stam
http://bioconductor.org/packages/2.4/bioc/html/stam.html
The stam package performs a biologically structured classification of microarray profiles according to clinical phenotypes. GO terms are used to link classification results to biological aspects.
modied version of the GLAD algorithm (Gain and Loss Analysis of DNA)
Fischer's Exact Test
This software implements a robust algorithm for spot finding and quantitation, quality metrics, and use of pre-made protocols ensure accuracy and reproducibility. Choices for background correction, normalization, and ratio calculation between arrays provides flexibility.Wizard guides simplify operation.Automatic batch processing increases throughput and saves time.Data easily exported to Microsoft™ Excel or database programs for flexibility in reporting.
ArrayVision
Nandini Badarinarayan
two-stage measurement error model
ImaGene 3.0
Nandini Badarinarayan
http://cran.r-project.org/web/packages/maanova/index.html
Tools for analyzing Micro Array experiments
MAANOVA v1.2 package for MATLAB
Nandini Badarinarayan
http://www.biocompare.com/ProductDetails/475470/ArrayAssist-Expression-Software-(1-year-academic-license).html
GC-RMA Quantification (Stratagene ArrayAssist Expression Software)
Single-user desktop software package for analyzing microarray data from multiple microarray platforms.
GC-RMA Quantification
Nandini Badarinarayan
An objective in which the aim is to create a new database instance.
James Malone
PERSON: James Malone
database creation objective
Walter and Eliza Hall Institute
'jpeg'
'Needleman-Wunsch'
http://www.cose.fr/us_dots.html
Analysis Software for Integrated Image Analysis for Spot Detection , Position and Quantification
XDotsReader
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/GSEAlm.html
Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics.
GSEAlm
Nandini Badarinarayan
Functions to visualize long vectors of integer data by means of Hilbert curves
http://bioconductor.org/packages/2.4/bioc/html/HilbertVis.html
Nandini Badarinarayan
HilbertVis
GASSCO method
negative binomial distribution
Multivariate correlation estimator
'ps'
BCRANK is a method that takes a ranked list of genomic regions as input and outputs short DNA sequences that are overrepresented in some part of the list.
BCRANK
R data frame
http://bioconductor.org/packages/2.4/bioc/html/BGmix.html
Bayesian models for differential gene expression
'BGmix'
Nandini Badarinarayan
Genepix pro 3.0
GenePix Pro 3.0
Nandini Badarinarayan
'dcf'
http://bioconductor.org/packages/2.4/bioc/html/clusterStab.html
Nandini Badarinarayan
This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters.
'clusterStab'
sim method
http://en.wikipedia.org/wiki/SAS_System
Statistical Analysis with a number of procedures, providing statistical information such as analysis of variance, regression, multivariate analysis, and categorical data analysis.
SAS/STAT Software, Version 8
Nandini Badarinarayan
Laplace mixture model
Radial basis function
Nandini Badarinarayan
'bioDist'
The bioDist package contains some distance functions that have been shown to be useful in a number of dierent biological or bioinformatic problems. The return values are typically instances of the S3 class dist.
http://bioconductor.org/packages/2.4/bioc/html/bioDist.html
Semantic Similarity Measures- Four methods proposed by Resnik[Philip, 1999], Jiang[Jiang and Conrath,
1997], Lin[Lin, 1998] and Schlicker[Schlicker et al., 2006] respectively have
presented to determine the semantic similarities of two GO terms based
on the annotation statistics of their common ancestor terms. Wang [Wang
et al., 2007] proposed a new method to measure the similarities based on
the graph structure of GO.
Semantic Similarity Measures
RMA+
Probe level Locally moderated Weighted median-t (PLW) method
A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made.
James Malone
PERSON: James Malone
decision tree induction objective
Estimation of local false discovery rate
http://bioconductor.org/packages/2.4/bioc/html/twilight.html
twilight
Nandini Badarinarayan
MAGE-TAB inputting software
Nandini Badarinarayan
Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries.
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/occugene.html
occugene
Complex Estimation Algorithm
gmt format
Agilent Feature Extraction software version 7.5
Nandini Badarinarayan
Raytest
http://bioconductor.org/packages/2.4/bioc/html/snpMatrix.html
snpMatrix
Implements classes and methods for large-scale SNP association studies
Nandini Badarinarayan
KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.
Nandini Badarinarayan
KEGGgraph
http://bioconductor.org/packages/2.4/bioc/html/KEGGgraph.html
http://bioconductor.org/packages/2.4/bioc/html/factDesign.html
'factDesign'
Nandini Badarinarayan
This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection.
Base-Pair-Distance Kernel
http://bioconductor.org/packages/2.4/bioc/html/OrderedList.html
Nandini Badarinarayan
OrderedList
Detection of similarities between ordered lists of genes. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively.
http://bioconductor.org/packages/2.4/bioc/html/GeneTraffic.html
Set of functions and class definitions to be able to read GeneTraffic specific data from a project summary zip file and covert them to BioConductor objects (for 1 color projects affy's ExpressionSet, for 2 color projects marray's marrayRaw)
GeneTraffic
Nandini Badarinarayan
Gene Recommender algorithm
http://maexplorer.sourceforge.net/MaeRefMan/hmaeDoc2.4.2.html
The background intensity data from the spot quantification programs may be used to correct spot intensity. This software measures background globally as: BGLow (low background), BGAvg (Average background), BGRms (root mean square background).
Pathways 2.01 software
Nandini Badarinarayan
Gamma Gamma Model
This package implements several functions useful for analysis of SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison
Nandini Badarinarayan
sagenhaft
http://bioconductor.org/packages/2.4/bioc/html/sagenhaft.html
Presence-Absence calls with Negative Probesets (PANP)
http://bioconductor.org/packages/2.4/bioc/html/GeneSpring.html
Set of functions and class definitions to be able to read and write GeneSpring specific data objects and covert them to BioConductor objects
GeneSpring
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/GSEABase.html
This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).
GSEABase
Nandini Badarinarayan
'sqlite'
http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf
MAS
Affymetrix MicroArraySuite
Affymetrix® Microarray Suite (MAS) is the core software product in the Affymetrix Software System providing instrument control, data acquisition, and data analysis for the entire GeneChip® platform.
MIcroarray Analysis Suite
Nandini Badarinarayan
Technique which predicts a given transcription factor activity and then uses this infor- mation to predict its targets.
Hidden Variable Dynamic Modelling HVDM)
GenePix 4100A [Axon Instruments]
GenePix 4100A
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/BufferedMatrix.html
This package creates a tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data.
'BufferedMatrix'
Nandini Badarinarayan
http://tagc.univ-mrs.fr/bioinformatics/bzscan/
BZScan is a free java tool for automatic quantification of DNA microarrays with radioactive labeling. BZScan provides saturation, overshining, and background noise correction, it also gives quality control measures. It can work either in a fully automatic "batch mode" or at different levels of manual operation.
BZScan
Nandini Badarinarayan
http://www.genedata.com/products/expressionist/overview.html
Genedata Expressionist® is an enterprise solution that integrates, stores and analyzes transcriptomics, proteomics and metabolomics data as well as a wide variety of phenotypic data.
GeneData Expressionist Analyst v4.0.5
Nandini Badarinarayan
PCMG- a bipartite graph in which one set of nodes represents proteins, the other set represents complexes, and an edge from a protein node to a complex node represents membership of the protein in that complex.
PCMG
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/CGHregions.html
Dimension Reduction for Array CGH Data with Minimal Information Loss
'CGHregions'
'ctc'
http://bioconductor.org/packages/2.4/bioc/html/ctc.html
Nandini Badarinarayan
Tools for export and import classification trees and clusters to other programs
GenePix Pro 6 [Axon Instruments]
Nandini Badarinarayan
Nandini Badarinarayan
OCplus
This package allows to characterize the operating characeristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes).
http://bioconductor.org/packages/2.4/bioc/html/OCplus.html
http://bioconductor.org/packages/2.4/bioc/html/SIM.html
Nandini Badarinarayan
SIM
Finds associations between DNA copy number and gene expression.
Absolute Expression Analysis
Nandini Badarinarayan
'CEL'
SAM
Theodore Ts’o’s
Nandini Badarinarayan
'flagme'
Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data
http://bioconductor.org/packages/2.4/bioc/html/flagme.html
gene list
FC
'flowFlowJo'
FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the "FlowJo Workspace". This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm.
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/flowFlowJo.html
Nandini Badarinarayan
The rama package consists of several functions for robust estimation of two color microarray intensities with replicates
rama
http://bioconductor.org/packages/2.4/bioc/html/rama.html
2
http://bioconductor.org/packages/2.4/bioc/html/MiPP.html
This package finds optimal sets of genes that seperate samples into two or more classes.
MiPP
Nandini Badarinarayan
Nandini Badarinarayan
genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer.
'genArise'
http://bioconductor.org/packages/2.4/bioc/html/genArise.html
Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting and data manipulation functions
propagation of uncertainty in microarray analysis
The circular binary segmentation (CBS) algorithm divides the genome into regions of equal copy number . The algorithm tests for change-points using a maximal t-statistic with a permutation reference distribution to obtain the corresponding p-value. The number of computations required for the maximal test statistic is O(N^2),where N is the number of markers. This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster algorithm.
CBS
gtr
cross validation objective
GlobalAncova
http://bioconductor.org/packages/2.4/bioc/html/GlobalAncova.html
Nandini Badarinarayan
GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values.
http://www.mathworks.com/products/matlab/?s_cid=SA_trafrefpai_MLipspot_Doc_bioinfo_MATLAB
MATLAB® is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran
MATLAB
Nandini Badarinarayan
Technological Advances for Genomics and Clinics, France
covdesc file
http://www.rosettabio.com/products/resolver
The Rosetta Resolver® system provides a central analysis center and repository for biologists, statisticians, and bioinformaticians for the evaluation of gene expression data from microarrays and qPCR studies.
Rosetta Resolver
Nandini Badarinarayan
k-nearest neighbour classification
Molecular Dynamics
Genicon Sciences
http://bioconductor.org/packages/2.4/bioc/html/idiogram.html
A package for plotting genomic data by chromosomal location
idiogram
Nandini Badarinarayan
Applied Precision Life Science
Signaling Pathway Impact Analysis (SPIA) algorithm
Nandini Badarinarayan
This package uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments
'BAC'
http://bioconductor.org/packages/2.4/bioc/html/BAC.html
GenePix Pro 3
Nandini Badarinarayan
A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.
James Malone
class discovery objective
Analysis of cell-based RNA interference screens
Nandini Badarinarayan
'cellHTS2'
http://bioconductor.org/packages/2.4/bioc/html/cellHTS2.html
This package provides a supervised technique able to identify differentially expressed genes. The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values.
'DFP'
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/DFP.html
Linear modelling
Institute for Genomics and Bioinformatics Graz University of Technology
iterative Bayesian Model Averaging (BMA)
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/iterativeBMA.html
iterativeBMA
The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples, as described in Yeung, Bumgarner and Raftery (Bioinformatics 2005, 21: 2394-2402).
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/rsbml.html
R support for SBML, using libsbml
rsbml
http://bioconductor.org/packages/2.4/bioc/html/tspair.html
Top Scoring Pairs for Microarray Classification
Nandini Badarinarayan
tspair
http://bioconductor.org/packages/2.4/bioc/html/affyPara.html
The package contains parallelized functions for exploratory oligonucleotide array analysis. The package is designed for large numbers of microarray data.
'affyPara'
Nandini Badarinarayan
Gamma-Gamma hierarchical model
dataset comparison objective
Serial Analysis of Gene Expression (SAGE)
genemeta
Nandini Badarinarayan
A collection of meta-analysis tools for analysing high throughput experimental data
http://bioconductor.org/packages/2.4/bioc/html/GeneMeta.html
http://bioconductor.org/packages/2.4/bioc/html/GeneMeta.html
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/HEM.html
HEM
This package fits heterogeneous error models for analysis of microarray data
Nandini Badarinarayan
XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
XDE
http://bioconductor.org/packages/2.4/bioc/html/XDE.html
Imagene v4.0
Nandini Badarinarayan
http://angiogenesis.dkfz.de/software/chipskipper/index.htm
ChipSkipper [EMBL]
ChipSkipper Microarray Data Evaluation Software
ChipSkipper - an integrated tool for analysis, evaluation and quantitation of DNA micro-array data
ChipSkipper
Nandini Badarinarayan
GraphAlignment
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/GraphAlignment.html
Graph alignment is an extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores.
ScanArray version 3.1
ScanArray v3.1 software
Nandini Badarinarayan
http://www.baymedia.com/gemtools/
Incyte GEMTools software is an enterprise solution for managing gene expression data using the SQL Server and Oracle relational databases. It was one of the first integrated software packages designed with an easy-to-use interface to help scientist track and analyze the vast amounts of gene expression data generated from microarray experiments. GEMTools can be used quantify and graphically display your gene expression data. Incyte Genomics relied on the GEMTools for internal operations and to track each well, probe, cDNA target, and other components of GEM arrays through ordering, fabrication, image analysis, and final data delivery.
GEMTools 2.4
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/EBImage.html
EBImage is an R package which provides general purpose functionality for the reading, writing, processing and analysis of images. Furthermore, in the context of microscopy based cellular assays, EBImage offers tools to transform the images, segment cells and extract quantitative cellular descriptors.
'EBImage'
Nandini Badarinarayan
Nandini Badarinarayan
Most analyses of Affymetrix GeneChip data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods.
puma
http://bioconductor.org/packages/2.4/bioc/html/puma.html
pdmclass
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/pdmclass.html
This package can be used to classify microarray data using one of three penalized regression methods; partial least squares, principal components regression, or ridge regression.
A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints.
James Malone
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
curve fitting objective
qPCR data
This algorithm offers improved confidence scores, quality scores for SNP’s and batches, higher accuracy on different datasets and better performance.
CRLMM algorithm
'cghMCR'
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/cghMCR.html
Based on the algothrim proposed by Dr. Lynda Chin's lab, this package provides functions that identify chromosome regions that show gains/losses commonly observed across different samples profiled using arrayCGH platform.
nnNorm
This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting.
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/nnNorm.html
http://bioconductor.org/packages/2.4/bioc/html/beadarray.html
The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.
'beadarray'
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/VanillaICE.html
Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays
Nandini Badarinarayan
VanillaICE
Nandini Badarinarayan
MantelCorr
http://bioconductor.org/packages/2.4/bioc/html/MantelCorr.html
Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data)
text data set
ILLUMINA data
http://bioconductor.org/packages/2.4/bioc/html/topGO.html
topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.
Nandini Badarinarayan
topGO
'MAQC data'
maDB allows to create a simple microarray database to store microarray experiments and annotation data into it. Affymetrix GeneChip expression values as well as values from two color microarrays can be stored into the database. Whole experiments or subsets from a experiment (or also values for a subset of genes in a subset of microarrays) can be fetched back to R. Additionally maDB provides different utility functions for the microarray data analysis like functions to draw MA plots or volcano plots with the data points color coded according to the local point density or functions that allow a replicate handling of miroarrays.
http://bioconductor.org/packages/2.4/bioc/html/maDB.html
Nandini Badarinarayan
maDB
GenePix 5.0.1
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/DEDS.html
'DEDS'
This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.
Nandini Badarinarayan
metaArray
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/metaArray.html
1) Data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) 2) Combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform
rtracklayer
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/rtracklayer.html
R interface to genome browsers and their annotation tracks
Lognormal Normal with Modied Variance Model
'MI'
2
http://bioconductor.org/packages/2.4/bioc/html/globaltest.html
Nandini Badarinarayan
globaltest
Testing whether sets of genes (e.g. KEGG pathways of GO terms) are significantly associated with a clinical variable of interest.
meta data
http://bioconductor.org/packages/2.4/bioc/html/Biobase.html
Functions that are needed by many other packages or which replace R functions
'Biobase'
Nandini Badarinarayan
log file
PLIER (Probe Logarithmic Error Intensity Estimate) method
http://bioconductor.org/packages/2.4/bioc/html/GeneRegionScan.html
A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data
GeneRegionScan
Nandini Badarinarayan
Harshlight
http://bioconductor.org/packages/2.4/bioc/html/Harshlight.html
The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitue value as whole matrix to solve the memory problem.
Nandini Badarinarayan
NIH
http://bioconductor.org/packages/2.4/bioc/html/RbcBook1.html
Support for Springer monograph on Bioconductor
RbcBook1
Nandini Badarinarayan
Nandini Badarinarayan
qvalue
This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant.
http://bioconductor.org/packages/2.4/bioc/html/qvalue.html
'affxparser'
http://bioconductor.org/packages/2.4/bioc/html/affxparser.html
Nandini Badarinarayan
affxparser is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK.
Applied Biosystems
http://bioconductor.org/packages/2.4/bioc/html/geneRecommender.html
geneRecommender
Nandini Badarinarayan
This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions.
http://bioconductor.org/packages/2.4/bioc/html/Ruuid.html
Ruuid
Nandini Badarinarayan
A package to provide UUID values in R
A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation.
James Malone
PERSON: Elisabetta Manduchi
background correction objective
.java file
'explorase'
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/explorase.html
This package explores and analyzes *omics data with R and GGobi
http://bioconductor.org/packages/2.4/bioc/html/DNAcopy.html
Segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number
'DNAcopy'
Nandini Badarinarayan
The iterative Bayesian Model Averaging (BMA) algorithm for survival analysis is a variable selection method for applying survival analysis to microarray data.
http://bioconductor.org/packages/2.4/bioc/html/iterativeBMAsurv.html
iterativeBMAsurv
Nandini Badarinarayan
't-test'
'MAS5'
distance calculation objective
quantile regression techniques
GE Healthcare Life Sciences
'AP-MS data'
gene array analysis algorithm
http://bioconductor.org/packages/2.4/bioc/html/widgetTools.html
This packages contains tools to support the construction of tcltk widgets
widgetTools
Nandini Badarinarayan
QuantArray version 2
Nandini Badarinarayan
AWS algorithm
http://bioconductor.org/packages/2.4/bioc/html/maCorrPlot.html
Graphically displays correlation in microarray data that is due to insufficient normalization
maCorrPlot
Nandini Badarinarayan
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm
'edd'
http://bioconductor.org/packages/2.4/bioc/html/edd.html
This package provides tools for evaluating cohort distributions of gene expression levels
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/Rdisop.html
Decomposition of Isotopic Patterns
Rdisop
Nandini Badarinarayan
PERSON: James Malone
PERSON: Elisabetta Manduchi
PERSON: Monnie McGee
mean calculation
A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
descriptive statistical calculation objective
James Malone
PERSON: Melanie Courtot
'Markov Chain Monte Carlo'
rda
http://bioconductor.org/packages/2.4/bioc/html/makePlatformDesign.html
makePlatformDesign creates the Platform Design environments (PDenvs) required by oligo.
makePlatformDesign
Nandini Badarinarayan
'pdf'
'HTML report'
Incyte Genomics
ALL/AML data set
WilcEbam
RNAither analyzes cell-based RNAi screens, and includes quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes
RNAither
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/RNAither.html
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/metahdep.html
Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies
metahdep
MMD describes the distributions of gene expression levels directly via the marginal distributions. It includes EM algorithm, FDR, it is the percentage of nondifferentially expressed genes among selected genes), false non-discovery rate (denoted as FNDR; it is the percentage of differentially expressed genes among unselected genes),false positive rate (denoted as FPR; it is the percentage of selected genes among nondifferentially expressed genes), and false negative rate (denoted as FNR; it is the percentage of un-selected genes among differentially expressed genes),
MMD
Median Average Difference Algorithm
http://bioconductor.org/packages/2.4/bioc/html/rHVDM.html
Hidden Variable Dynamic Modeling
Nandini Badarinarayan
rHVDM
Nandini Badarinarayan
A package that implements some simple graph handling capabilities.
graph
http://bioconductor.org/packages/2.4/bioc/html/graph.html
SAS Institute Inc.
EBarrays provides tools for the analysis of replicated/unreplicated microarray data.
http://bioconductor.org/packages/2.4/bioc/html/EBarrays.html
'EBarrays'
Nandini Badarinarayan
A material entity is a real world physical object. It is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray.
James Malone
A material entity is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray.
material entity
hypergeometric enrichment
'Smith-Waterman'
A package for processing protein mass spectrometry data.
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/PROcess.html
PROcess
CMA- it implements k-fold cross validation, MCMC cross validation, bootstrap and (t.test or welch.test or wilcox.test or f.test or kruskal.test or One-step Recursive Feature Elimination or random forest variable importance measure or lasso or elastic net or componentwise boosting)
CMA
plgem
http://bioconductor.org/packages/2.4/bioc/html/plgem.html
PLGEM is useful for detecting differential expression in microarray and proteomics datasets.
Nandini Badarinarayan
Cambridge Bluegnome
http://bioconductor.org/packages/2.4/bioc/html/multtest.html
Resampling-based multiple hypothesis testing
multtest
Nandini Badarinarayan
COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles.
Nandini Badarinarayan
'copa'
http://bioconductor.org/packages/2.4/bioc/html/copa.html
cdt
parse objective
.raw files
Loess algorithm
'graphs'
for the Support Vector Machine (SVM), as presented in [3] and the Nearest Shrunken Centroid (NSC)
Recursive Feature Elimination (RFE)
PPC algorithm
pedigree data file
Array_vision_(Interfocus)
Nandini Badarinarayan
Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, EIC correlation based tagging of unknown adducts and fragments
'CAMERA'
Nandini Badarinarayan
Havard School of Public Health
A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons.
James Malone
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Helen Parkinson
data normalization objective
SNPRMA algorithm
Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids.
'ecolitk'
http://bioconductor.org/packages/2.4/bioc/html/ecolitk.html
Nandini Badarinarayan
ArrayExpress Bioconductor package is software that read in MAGE-TAB format files from the ArrayExpress FTP site and converts them to R objects.
http://bioconductor.org/packages/2.4/bioc/html/ArrayExpress.html
ArrayExpress Bioconductor
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/affycomp.html
affycomp
Nandini Badarinarayan
The affycomp package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.
BaldiLongT
http://bioconductor.org/packages/2.4/bioc/html/bgafun.html
BGAfun is a method to identify specifity determining residues in protein families
'bgafun'
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/reb.html
A set of functions to dentify regional expression biases
reb
Nandini Badarinarayan
This library contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. MACAT is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions. The functions have been tested on a publicly available data set about acute lymphoblastic leukemia (Yeoh et al.Cancer Cell 2002), which is provided in the library 'stjudem'.
Nandini Badarinarayan
macat
http://bioconductor.org/packages/2.4/bioc/html/biocViews.html
Categorized views of R package repositories
'biocViews'
Nandini Badarinarayan
Nandini Badarinarayan
'codelink'
http://bioconductor.org/packages/2.4/bioc/html/codelink.html
This packages allow reading into R of Codelink bioarray data exported as text from the Codelink software. Also includes some functions to ease the manipulation and pre-processing of data, such in background correction and normalization.
http://bioconductor.org/packages/2.4/bioc/html/seqLogo.html
Nandini Badarinarayan
seqLogo
seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo
http://bioconductor.org/packages/2.4/bioc/html/arrayQualityMetrics.html
This package generates a quality metrics report on ExpressionSet, NChannelSet, AffyBatch or BeadLevelList objects containing microarray data with one or two channels.
'arrayQualityMetrics'
Nandini Badarinarayan
Add an extra graphical display at the bottom of a heat map, indicating for each column a) whether it has one of several binary properties or not, and b) the value of a quantitative variable. A cutting threshold for the sample dendrogram can also be specified, and the resulting clustering of the columns is indicated by coloring both the dendrogram and the extra variable display.
Heatplus
http://bioconductor.org/packages/2.4/bioc/html/Heatplus.html
Nandini Badarinarayan
pair file
A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself.
PERSON: James Malone
PERSON: Melanie Courtot
correction objective
http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/dnamicroarrayscanner/pages/default.aspx
High resolution scanning with pixel sizes of 2, 3, 5, and 10 microns enables users to scan a range of array types from ultra-high density commercial arrays as well as low-density home-brew arrays.Low level detection resulting from optimized precision optics, broad dynamic range, minimal spectral cross talk allowing users to detect weak features, achieve rapid, accurate and dependable results
Scanning software G2565AA version A6.3.1
Nandini Badarinarayan
A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
PERSON: Alan Ruttenberg
data format specification
GeneSpringGX
Nandini Badarinarayan
multinomial probit regression with Gaussian Process priors
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/CGHcall.html
'CGHcall'
Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided.
Nonlinear Estimation by Iterative Partial Least Squares
Speed Berkeley Research Group
annotation data packages
http://dmaf.biochem.uci.edu/affymetrix_analysis_software.html
Cyber-T may be used to statistically determine what the probability is that a specific gene is differentially expressed by determining an associated p-value statistic.
Cyber-T
Nandini Badarinarayan
A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image.
feature extraction objective
An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
James Malone
averaging objective
http://bioconductor.org/packages/2.4/bioc/html/arrayMvout.html
This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate
'arrayMvout'
Nandini Badarinarayan
mutual information matrix (MIM)
http://www.moleculardevices.com/pages/software/gn_genepix_pro.html
Genepix
Gene Pix
GenePix is the industry standard microarray image analysis software because of its unique combination of imaging and analysis tools, visualizations, automation capabilities, performance and ease of use.
Gene Pix
Nandini Badarinarayan
Gene-Set Enrichment Analysis
http://bioconductor.org/packages/2.4/bioc/html/PGSEA.html
Parametric Analysis of Gene Set Enrichment
PGSEA
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/KEGGSOAP.html
A package that provides a client interface to the KEGG SOAP server
KEGGSOAP
Nandini Badarinarayan
Continuous Wavelet Transform (CWT)-based peak detection algorithm
http://www.cambridgebluegnome.com/bluefuse.htm
BlueFuse [BlueGnome]
BlueFuse for Microarrays is a powerful software solution for the analysis of microarray expression and arrayCGH experiments. Operation is simple and fully automated, saving time, removing operator error and subjectivity and ensuring experimental reproducibility.
BlueFuse
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/OutlierD.html
Nandini Badarinarayan
OutlierD
This package detects outliers using quantile regression on the M-A scatterplots of high-throughput data.
Nandini Badarinarayan
This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes.
http://bioconductor.org/packages/2.4/bioc/html/miRNApath.html
miRNApath
RMAExpress quantification
Nandini Badarinarayan
A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
objective specification
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/quantsmooth.html
Quantile smoothing and genomic visualization of array data
quantsmooth
Fujifilm
Jaccard’s index
http://www.clontech.com/images/pacs/634650-PA27475.pdf
Computer software for the analysis and comparison of Atlas™ nylon and plastic arrays.
AtlasImage
Nandini Badarinarayan
https://carmaweb.genome.tugraz.at/carma/
CarmaWEB
CARMAweb allows the analysis of Affymetrix GeneChip, ABI microarrays and two color microarrays.
The analysis includes normalization and data preprocessing, detection for differentially expressed genes, cluster analysis and GO analysis. All calculations (except the cluster analysis) are performed in R using functions provided by the BioConductor packages.
CARMAweb
Nandini Badarinarayan
ICS-501 (version 2.3) Image Capture System
Nandini Badarinarayan
https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600530
Genetic Analyzer is a multi-color fluorescence-based DNA analysis system with 16 capillaries operating in parallel, offers high-quality data and efficient sample processing
GeneTac Analyser
Nandini Badarinarayan
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/pcot2.html
pcot2
PCOT2 is a permutation-based method for investigating changes in the activity of multi-gene networks. It utilizes inter-gene correlation information to detect significant alterations in gene network activities. Currently it can be applied to two-sample comparisons.
http://bioconductor.org/packages/2.4/bioc/html/xmapbridge.html
xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format.
xmapbridge
Nandini Badarinarayan
http://www.bio-medicine.org/
VersArray ChipReader
Versarray ChipReader systems are highly sensitive laser confocal systems designed for rapid imaging of microarrays. These are advanced scanners that meet your expectations, differentiating between a spot response and background level, and optimizing the signal on the bottom as well as the top end of the range for increased sensitivity. Results with versarray chipreader systems have a low background, enhanced weak signal detection, and virtually no photobleaching for a long dye lifetime.
ChipReader 3.1
Nandini Badarinarayan
Mixed model equations
Multi sample aCGH analysis package using kernel convolution
http://bioconductor.org/packages/2.4/bioc/html/KCsmart.html
KCsmart
Nandini Badarinarayan
http://www.tm4.org/contributors.html
TIGR Spotfinder was designed for the rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression
Spotfinder [TIGR]
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/SLGI.html
A variety of data files and functions for the analysis of genetic interactions
SLGI
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/AnnotationDbi.html
This package provides user interface and database connection code for annotation data packages using SQLite data storage.
'AnnotationDbi'
Nandini Badarinarayan
Nandini Badarinarayan
Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search
http://bioconductor.org/packages/2.4/bioc/html/BCRANK.html
'BCRANK'
http://bioconductor.org/packages/2.4/bioc/html/gaggle.html
This package contains functions connecting R with the Gaggle
'gaggle'
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/BufferedMatrixMethods.html
This package involves microarray Data related methods that utlize BufferedMatrix objects
'BufferedMatrixMethods'
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/Ringo.html
Ringo
The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data visualisation and identification of genomic regions showing enrichment in ChIP-chip. The package has functions to deal with two-color oligonucleotide microarrays from NimbleGen used in ChIP-chip projects
2
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/BSgenome.html
This document describes the process of forging a BSgenome data package. It is intended for Bioconductor
users who want to make a new BSgenome data package
'BSgenome'
Nandini Badarinarayan
CLR algorithm
minimum common regions (MCR) algorithm- Minimal common regions (MCRs) are dened as contiguous spans having at least a recurrence rate dened by a parameter (recurrence) across samples.
MCR algorithm
http://bioconductor.org/packages/2.4/bioc/html/affypdnn.html
The package contains functions to perform the PDNN method described by Li Zhang et al.
'affypdnn'
Nandini Badarinarayan
logicFS dataset
http://bioconductor.org/packages/2.4/bioc/html/pkgDepTools.html
This package provides tools for computing and analyzing dependency relationships among R packages. It provides tools for building a graph-based representation of the dependencies among all packages in a list of CRAN-style package repositories. There are also utilities for computing installation order of a given package. If the RCurl package is available, an estimate of the download size required to install a given package and its dependencies can be obtained.
pkgDepTools
Nandini Badarinarayan
Wilcoxon
Gaussian locally weighted regression
Bahler Lab
http://bioconductor.org/packages/2.4/bioc/html/CMA.html
'CMA'
Nandini Badarinarayan
This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment.
algorithm
'plots'
'domainsignatures'
Nandini Badarinarayan
Find significantly enriched gene classifications in a list of functionally undescribed genes based on their InterPro domain structure.
http://bioconductor.org/packages/2.4/bioc/html/domainsignatures.html
Library Search Algorithm
The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications
Nandini Badarinarayan
HELP
http://bioconductor.org/packages/2.4/bioc/html/HELP.html
MATLAB
http://www.affymetrix.com
Affymetrix GCOS software
The Affymetrix GeneChip Operating Software (GCOS) is an operating system software that controls Affymetrix instruments, acquires data, and executes gene expression analysis. In addition, GCOS contains an embedded database that manages both experiment information and data.
Nandini Badarinarayan
GCOS software
Affymetrix GeneChip Operating Software
GeneChip Operating Software
avgNRRs
http://bioconductor.org/packages/2.4/bioc/html/BiocCaseStudies.html
Software and data to support the case studies.
'BiocCaseStudies'
Nandini Badarinarayan
Nandini Badarinarayan
This package implements a Kolmogorov Smirnov rank-sum based algorithm for training and classification of gene expression data sets. One of the chief strengths of this approach is that it is amenable to the "multiclass" problem. That is, it can discriminate between more than 2 classes.
'dualKS'
http://bioconductor.org/packages/2.4/bioc/html/dualKS.html
http://bioconductor.org/packages/2.4/bioc/html/SSPA.html
Sample size and power analysis for microarray data, where two groups are analysed.
SSPA
Nandini Badarinarayan
Hidden Markov Model
newick
http://bioconductor.org/packages/2.4/bioc/html/Rtreemix.html
Nandini Badarinarayan
Rtreemix
Rtreemix is a package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. It includes functions for fitting the trees mixture models, likelihood computations, model comparisons, waiting time estimations, stability analysis, etc.
Firth's bias reduction procedure
http://bioconductor.org/packages/2.4/bioc/html/splicegear.html
A set of tools to work with alternative splicing
splicegear
Nandini Badarinarayan
GeneticsPed
Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities. Note that package is not yet stable
http://bioconductor.org/packages/2.4/bioc/html/GeneticsPed.html
Nandini Badarinarayan
Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods.
http://bioconductor.org/packages/2.4/bioc/html/hexbin.html
Nandini Badarinarayan
hexbin
GenePix 4.1
Nandini Badarinarayan
FACS data
http://www.biodiscovery.com/index/imagene
Imagene
ImaGene [BioDiscovery]
ImaGene microarray image analysis software by biodiscovery for microarrays, protein arrays and CGH analysis.
ImaGene
Nandini Badarinarayan
local-pooled-error
http://bioconductor.org/packages/2.4/bioc/html/timecourse.html
Nandini Badarinarayan
timecourse
Functions for data analysis and graphical displays for developmental microarray time course data.
'M-estimation regression'
Agilent Feature Extraction software version A.5.1.1
Nandini Badarinarayan
Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg.
http://bioconductor.org/packages/2.4/bioc/html/pdInfoBuilder.html
Nandini Badarinarayan
pdInfoBuilder
The splots package provides the plotScreen function for the visualization of for high-throughput assays in microtitre plate or chamber slide format.
http://bioconductor.org/packages/2.4/bioc/html/splots.html
Nandini Badarinarayan
splots
FCS
Algorithms for Calculating Microarray Enrichment
Nandini Badarinarayan
ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.
http://bioconductor.org/packages/2.4/bioc/html/ACME.html
Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations.
http://bioconductor.org/packages/2.4/bioc/html/Rmagpie.html
Nandini Badarinarayan
Rmagpie
SBMLR file
http://bioconductor.org/packages/2.4/bioc/html/TypeInfo.html
A prototype for a mechanism for specifying the types of parameters and the return value for an R function. This is meta-information that can be used to generate stubs for servers and various interfaces to these functions
TypeInfo
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/Biostrings.html
Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or set of sequences.
'Biostrings'
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/CALIB.html
'CALIB'
Nandini Badarinarayan
This package contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estiamted from external control spikes.
Absolute Expression Analysis
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/oligoClasses.html
This package contains class definitions, validity checks, and initialization methods for classes used by the oligo package.
oligoClasses
Nandini Badarinarayan
FARMS
The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level.
Nandini Badarinarayan
lumi
http://bioconductor.org/packages/2.4/bioc/html/lumi.html
The ACME algorithm is quite straightforward. Using a user-dened quantile of the data,called the threshold, any probes in the data that are above that threshold are considered positive probes. A p-value is then assigned to each probe.
'ACME'
csv data set
MeasurementError.cor
Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation
http://bioconductor.org/packages/2.4/bioc/html/MeasurementError.cor.html
Nandini Badarinarayan
'lma'
Functions to Analyze Microarray (Gene Expression) Data.
Nandini Badarinarayan
pickgene
http://bioconductor.org/packages/2.4/bioc/html/pickgene.html
http://bioconductor.org/packages/2.4/bioc/html/Rgraphviz.html
Provides plotting capabilities for R graph objects
Rgraphviz
Nandini Badarinarayan
Stepwise normalization functions for cDNA microarray data.
http://bioconductor.org/packages/2.4/bioc/html/stepNorm.html
Nandini Badarinarayan
stepNorm
chi-square
Nandini Badarinarayan
Methods for estimating GO semantic similarities. Implemented five methods proposed by Resnik, Schlicker(Rel), Jiang, Lin and Wang respectively. Support five species: human, rat, mouse, fly, and yeast.
http://bioconductor.org/packages/2.4/bioc/html/GOSemSim.html
GOSemSim
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=101854
This software has a series of analytical tools to address the manufacturing, detection and data analysis components of a microarray experiment. Together, these tools help optimize performance in an expression profiling study.
CodeLink Expression Analysis Software
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/prada.html
Nandini Badarinarayan
prada
Tools for analysing and navigating data from high-throughput phenotyping experiments based on cellular assays and fluorescent detection (flow cytometry (FACS), high-content screening microscopy).
http://www.bioconductor.org/packages/release/Software.html
Convenience data structures and functions to handle cdfenvs
'altcdfenvs'
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/GEOmetadb.html
The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata.
GEOmetadb
Nandini Badarinarayan
pgUtils
Functions for creating PostgreSQL database tables, with auto incrementing primary keys, selection of foreign keys to allow referencial integrity and a logging mechanism.
http://bioconductor.org/packages/2.4/bioc/html/pgUtils.html
Nandini Badarinarayan
Hardy-Weinberg equilibrium
Expectation-Maximization(EM) algorithm
maSigPro
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/maSigPro.html
maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments.
This package contains a systems biology markup language (SBML) interface and biochemical system analysis tools with illustrative examples.
http://bioconductor.org/packages/2.4/bioc/html/SBMLR.html
Nandini Badarinarayan
SBMLR
'annotationTools'
http://bioconductor.org/packages/2.4/bioc/html/annotationTools.html
Nandini Badarinarayan
This package functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files).
gene expression analysis objective
http://bioconductor.org/packages/2.4/bioc/html/externalVector.html
Basic class definitions and generics for external pointer based vector objects for R. A simple in-memory implementation is also provided
'externalVector'
Nandini Badarinarayan
University Of California, Berkeley
http://www.raytest.de/index2.html
AIDA is a modular software package for evaluation and documentation of images that were obtained with digital devices such as CCD cameras, flat bed scanners, or BAS / FLA- scanners from Fuji. Additionally, AIDA allows the loading of loading a variety of images in other image formats (e.g.: TIFF, JPEG, Bmp, gel). AIDA can control all scanning devices offering a TWAIN compatible driver.
AIDA
Nandini Badarinarayan
Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/affycoretools.html
'affycoretools'
Agilent Feature Extraction 5.1.1
Nandini Badarinarayan
Fixed effect model
F test
http://bioconductor.org/packages/2.4/bioc/html/pathRender.html
pathRender
build graphs from pathway databases, render them by Rgraphviz
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/RWebServices.html
This package provides mechanisms for automatic function prototyping and exposure of R functionality in a web services environment.
RWebServices
Nandini Badarinarayan
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/crlmm.html
Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 6.0.
'crlmm'
LMGene package for analysis of microarray data using a linear model and glog data transformation in the R statistical package
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/LMGene.html
LMGene
http://bioconductor.org/packages/2.4/bioc/html/SAGx.html
A package for retrieval, preparation and analysis of data from the Affymetrix GeneChip. In particular the issue of identifying differentially expressed genes is addressed.
SAGx
Nandini Badarinarayan
Dynamic programming algorithm
MAGE-ML files
http://blast.ncbi.nlm.nih.gov/Blast.cgi
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
BLAST
Nandini Badarinarayan
variance-stabilizing transformation (VST) algorithm
Bio Discovery
digital gene expression (DGE) datasets
Power Law Global Error Model (PLGEM) analysis method
Nandini Badarinarayan
Tools for operation on genomic intervals.
genomeIntervals
http://bioconductor.org/packages/2.4/bioc/html/genomeIntervals.html
PCpheno
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/PCpheno.html
Tools to integrate, annotate, and link phenotypes to cellular organizational units such as protein complexes and pathways.
Nandini Badarinarayan
siggenes
Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).
http://bioconductor.org/packages/2.4/bioc/html/siggenes.html
http://bioconductor.org/packages/2.4/bioc/html/spkTools.html
Nandini Badarinarayan
The package contains functions that can be used to compare expression measures on different array platforms.
spkTools
A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations
http://bioconductor.org/packages/2.4/bioc/html/GOstats.html
GOstats
Nandini Badarinarayan
http://www.stat.berkeley.edu/users/terry/zarray/Software/smacode.html
Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments.
R software
Nandini Badarinarayan
R language
GenePix Pro 5.0
Nandini Badarinarayan
'images'
http://bioconductor.org/packages/2.4/bioc/html/parody.html
Routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics
parody
Nandini Badarinarayan
http://purl.obolibrary.org/obo/OBI_0000245
An organization is a continuant entity which can play roles, has
members, and has a set of organization rules. Members of organizations
are either organizations themselves or individual people. Members can
play specific organization member roles that are determined in the
organization rules. The organization rules also determine how decisions
are made on behalf of the organization by the organization members.
organization
http://bioconductor.org/packages/2.4/bioc/html/RdbiPgSQL.html
Provides methods for accessing data stored in PostgreSQL tables.
RdbiPgSQL
Nandini Badarinarayan
Random effects model
'BED file'
Robust likelihood-based survival modeling
'diffGeneAnalysis'
http://bioconductor.org/packages/2.4/bioc/html/diffGeneAnalysis.html
Nandini Badarinarayan
Analyze microarray data
Scanning software
Nandini Badarinarayan
GenePix Pro 6.0
Nandini Badarinarayan
Gene selection based on a mixture of marginal distributions
GeneSelectMMD
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/GeneSelectMMD.html
Functions and datasets and examples to accompany the monograph R For Bioinformatics.
Nandini Badarinarayan
RBioinf
http://bioconductor.org/packages/2.4/bioc/html/RBioinf.html
associative T method
http://bioconductor.org/packages/2.4/bioc/html/makecdfenv.html
This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment.
makecdfenv
Nandini Badarinarayan
neural networks models
iterative local regression and model selection
Hypergeometric probability
'KLD'
Gene-specific dye-bias correction of two-color microarray data using the GASSCO method
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/dyebias.html
'dyebias'
http://bioconductor.org/packages/2.4/bioc/html/SNPchip.html
SNPchip
Nandini Badarinarayan
This package defines classes and functions for plotting copy number and genotype in high throughput SNP platforms such as Affymetrix and Illumina. In particular, SNPchip is a useful add-on to the oligo package for visualizing SNP-level estimates after pre-processing.
This package uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data
maigesPack
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/maigesPack.html
http://bin.tugraz.at/Tools/ArrayNorm.html
ArrayNorm is an platform-independent Java tool for normalization and statistical analysis for microarray-experiment data. It provides modules for visualization (scatterplot, histogram, boxplot, etc.), normalization and analysis.
ArrayNorm
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/sigPathway.html
Conducts pathway analysis by calculating the NT_k and NE_k statistics
sigPathway
Nandini Badarinarayan
hexagon binning algorithm
binning clustering method- The algorithm uses single-linkage clustering to join compounds into similarity groups, where every member in a cluster shares with at least one other member a similarity value above a user-specified threshold. The algorithm is optimized for speed and memory
eciency by avoiding the calculation of an all-against-all distance matrix.
Binning clustering method
SVDimpute algorithm
AMDIS
chamber slide format
'png'
Contains functions and classes that are needed by arrayCGH packages.
Nandini Badarinarayan
'CGHbase'
http://bioconductor.org/packages/2.4/bioc/html/CGHbase.html
http://bioconductor.org/packages/2.4/bioc/html/cosmo.html
Nandini Badarinarayan
cosmo searches a set of unaligned DNA sequences for a shared motif that may, for example, represent a common transcription factor binding site. The algorithm is similar to MEME, but also allows the user to specify a set of constraints that the position weight matrix of the unknown motif must satisfy. Such constraints may include bounds on the information content across certain regions of the unknown motif, for example, and can often be formulated on the basis of prior knowledge about the structure of the transcription factor in question. The unknown motif width, the distribution of motif occurrences (OOPS, ZOOPS, or TCM), as well as the appropriate constraint set can be selected data-adaptively.
'cosmo'
http://bioconductor.org/packages/2.4/bioc/html/RMAGEML.html
This package can be used to handle MAGEML documents in Bioconductor
RMAGEML
Nandini Badarinarayan
Nandini Badarinarayan
Reverse engineering of molecular regulatory networks with qp-graphs
http://bioconductor.org/packages/2.4/bioc/html/qpgraph.html
qpgraph
MAGE-TAB is a tab delimited data format comprimising of ADF file for array design, IDFfor experimental design, SDRF for sample data relationships and associated data files.
MAGE-TAB
Dana-Farber Cancer Institute and Harvard School of Public Health
A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
James Malone
center calculation objective
cosmo allows the user to target the motif search by specifying a set of constraints that the unknown position weight matrix must satisfy. The algorithm is based on a probabilistic model that describes the DNA sequences of interest through a two- component multinomial mixture model with estimates of the position weight matrix entries obtained by maximizing the observed data likelihood over the smaller parameter space corresponding to the imposed constraints. It includes methods such as Probabilistic models and one-occurrence-per-sequence and zero-or-one-occurrence-per-sequence and two-component mixture
cosmo
tilingArray
http://bioconductor.org/packages/2.4/bioc/html/tilingArray.html
Transcript mapping with high-density oligonucleotide tiling arrays
Nandini Badarinarayan
Genedata
.data
This package contains an implementation of the S-Score algorithm
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/sscore.html
sscore
MVCClass
Creates classes used in model-view-controller (MVC) design
http://bioconductor.org/packages/2.4/bioc/html/MVCClass.html
Nandini Badarinarayan
Regression model
Nandini Badarinarayan
lapmix
http://bioconductor.org/packages/2.4/bioc/html/lapmix.html
Nandini Badarinarayan
gene2pathway
http://bioconductor.org/packages/2.4/bioc/html/gene2pathway.html
The package takes a list of genes and predicts to which KEGG pathway each gene maps to. This is done by looking at the InterPro domains of each gene. Each prediction is assigned a confidence score. The package also allows to predict connected component membership of genes within signaling pathways. Separate models for each organism supported by KEGG can be trained.
http://bioconductor.org/packages/2.4/bioc/html/GeneR.html
Package manipulating nucleotidic sequences (Embl, Fasta, GenBank)
GeneR
Nandini Badarinarayan
Affymetrix Software
Nandini Badarinarayan
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/rbsurv.html
This package selects genes associated with survival.
rbsurv
BGL implements Depth First Search, Breadth First Search,Dijkstra's, Bellman Ford's and DAG,Johnson's and Floyd Warshall's.Kruskal's algorithm and Prim's algorithm Cuthill-McKee's algorithm Minimum degree Ordering
BGL
SBML file
http://bioconductor.org/packages/2.4/bioc/html/rflowcyt.html
Statistical tools and data structures for analytic flow cytometry
rflowcyt
Nandini Badarinarayan
Motorola Life Sciences
http://bioconductor.org/packages/2.4/bioc/html/Rdbi.html
Generic database methods
Rdbi
Nandini Badarinarayan
'edgeR'
Estimation and Testing for Differential Expression in Multiple Digital Gene Expression Libraries.
http://bioconductor.org/packages/2.4/bioc/html/edgeR.html
Nandini Badarinarayan
GenePix 3.0.6
Nandini Badarinarayan
RMAExpress 2.0
Nandini Badarinarayan
Mahalanobis distance
http://bioconductor.org/packages/2.4/bioc/html/daMA.html
'daMA'
This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data.
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/AffyTiling.html
This package provides easy, fast functions for the extraction and annotation of individual probes from Affymetrix tiling arrays.
Nandini Badarinarayan
'affyTiling'
An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself.
James Malone
PERSON: James Malone
error correction objective
ChemMineR is an open source compound mining framework. It contains functions for atom descriptor calculation, structure similarity searching, clustering of compound libraries and various utilities for managing complex compound data. It also offers a wide range of visualization functions for compound clusters and chemical structures. The package is integrated with the online ChemMine environment and allows bidirectional communications between the two services.
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/ChemmineR.html
'ChemmineR'
qpcrNorm
http://bioconductor.org/packages/2.4/bioc/html/qpcrNorm.html
Nandini Badarinarayan
The package contains functions to perform normalization of high-throughput qPCR data. Basic functions for processing raw Ct data plus functions to generate diagnostic plots are also available.
Spot quantification
Nandini Badarinarayan
http://las.perkinelmer.com/content/relatedmaterials/brochures/bro_quantarray.pdf
QuantArray
QuantArray® is a powerful microarray analysis software that enables researchers to
easily and accurately visualize and quantitate gene expression data.
QuantArray scanner software
Nandini Badarinarayan
GMS
Nandini Badarinarayan
This packages provides a targeted pre-processing method for GC-MS data.
http://bioconductor.org/packages/2.4/bioc/html/TargetSearch.html
TargetSearch
Nandini Badarinarayan
Agilent Feature Extraction software version 7.1
Nandini Badarinarayan
LC-MS data
J. Craig Venter Institute
Axon GenePix Pro
GenePix Pro [Axon Instruments]
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/matchprobes.html
Basic infrastructure for using oligonucleotide microarray reporter sequence information for preprocessing and quality assessment. For general work with genomic sequences, this package is inadequate. Please refer to the Biostrings package for that.
matchprobes
Nandini Badarinarayan
The IRanges class and its extensions are low-level containers for storing sets of integer ranges. A typical use of these containers in biology is for representing a set of chromosome regions. More specific extensions of the IRanges class will typically allow the storage of additional information attached to each chromosome region as well as a hierarchical relationship between these regions.
http://bioconductor.org/packages/2.4/bioc/html/IRanges.html
IRanges
Nandini Badarinarayan
Agilent Technologies Software
Nandini Badarinarayan
Analysis of N-dye Micro Array experiment using mixed model effect. Containing anlysis of variance, permutation and bootstrap, cluster and consensus tree.
Nandini Badarinarayan
maanova
http://bioconductor.org/packages/2.4/bioc/html/maanova.html
http://bioconductor.org/packages/2.4/bioc/html/biocGraph.html
This package provides examples and code that make use of the different graph related packages produced by Bioconductor.
'biocGraph'
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/ontoTools.html
tools for working with ontologies and graphs
ontoTools
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/logitT.html
The logitT library implements the Logit-t algorithm introduced in --A high performance test of differential gene expression for oligonucleotide arrays-- by William J Lemon, Sandya Liyanarachchi and Ming You for use with Affymetrix data stored in an AffyBatch object in R.
logitT
Nandini Badarinarayan
goTools
http://bioconductor.org/packages/2.4/bioc/html/goTools.html
Nandini Badarinarayan
Wraper functions for description/comparison of oligo ID list using Gene Ontology database
http://bioconductor.org/packages/2.4/bioc/html/mdqc.html
mdqc
MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality.
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/affy.html
Nandini Badarinarayan
The affy package contains functions for exploratory oligonucleotide array analysis. The dependance to tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
affy
http://bioconductor.org/packages/2.4/bioc/html/bgx.html
Bayesian integrated analysis of Affymetrix GeneChips
'bgx'
Nandini Badarinarayan
Similarity score
http://bioconductor.org/packages/2.4/bioc/html/GeneticsDesign.html
This package contains functions useful for designing genetics studies, including power and sample-size calculations.
GeneticsDesign
Nandini Badarinarayan
A collection of software tools for dealing with co-citation data.
Nandini Badarinarayan
'CoCiteStats'
http://bioconductor.org/packages/2.4/bioc/html/CoCiteStats.html
Nandini Badarinarayan
A package that implements some simple capabilities for representing and manipulating hypergraphs.
hypergraph
http://bioconductor.org/packages/2.4/bioc/html/hypergraph.html
FoxDimmicT
http://bioconductor.org/packages/2.4/bioc/html/ssize.html
Functions for computing and displaying sample size information for gene expression arrays.
ssize
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/GEOquery.html
The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of these data, it is only natural to want to apply BioConductor tools to these data.
GEOquery
Nandini Badarinarayan
Pearson correlation estimator
Nandini Badarinarayan
This package fits Rossell's generalizations of the Gamma-Gamma hierarchical model for microarray data analysis, which substantially improve the quality of the fit at a low computational cost. The model can be fit via empirical Bayes (Expectation-Maximization and Simulated Annealing) and fully Bayesian techniques (Gibbs and Metropolis-Hastings posterior sampling).
'gaga'
http://bioconductor.org/packages/2.4/bioc/html/gaga.html
likelihood method
http://www.research.bidmc.harvard.edu/AcademicIT/ImageQuant.asp
ImageQuant (Molecular Dynamics)
This is a general image analysis program used in the study of electrophoretic separations, dot blots, slot blots, microplate assays, TLC assays, and plaque assays. ImageQuant provides a point-and-click environment for fast analysis of qualitative and quantitative assays. With tools for accurate volume integration, ImageQuant generates accurate lane profiles even for curved or slanted lanes.
ImageQuant
Nandini Badarinarayan
http://www.illumina.com/pages.ilmn?ID=35
BeadStudio Software is a modular analysis tool for genotyping, gene expression, and methylation applications
Beadstudio
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/MCRestimate.html
This package includes a function for combining preprocessing and classification methods to calculate misclassification errors
MCRestimate
Nandini Badarinarayan
Langmuir Isotherm
http://bioconductor.org/packages/2.4/bioc/html/spotSegmentation.html
Spot segmentation via model-based clustering and gridding for blocks within microarray slides
Nandini Badarinarayan
spotSegmentation
The aCGH package functions for reading data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.
Nandini Badarinarayan
Array Comparative Genomic Hybridization
http://bioconductor.org/packages/2.4/bioc/html/aCGH.html
clustering algorithm
non-linear functional regression model with both additive and multiplicative error terms
non-linear functional regression model
mrnet algorithm
Stanford University
http://bioconductor.org/packages/2.4/bioc/html/flowViz.html
Provides visualization tools for flow cytometry data
'flowViz'
Nandini Badarinarayan
Uniform interfaces to machine learning code for data in Bioconductor containers
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/MLInterfaces.html
MLInterfaces
design file
http://www.bioconductor.org/overview
Nandini Badarinarayan
Bioconductor is an open source and open development software project to provide tools for the analysis and comprehension of genomic data. Bioconductor is based primarily on the R programming language, but does contain contributions in other programming languages.
Bioconductor
BioConductor Software
http://purl.obolibrary.org/obo/IAO_0000129
A version number is information which is a sequence of characters about a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
version number
James Malone
http://bioconductor.org/packages/2.4/bioc/html/flowStats.html
'flowStats'
Nandini Badarinarayan
This package contains methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package.
Nandini Badarinarayan
marray
Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.
http://bioconductor.org/packages/2.4/bioc/html/marray.html
MathWorks
http://www.fujifilm.com/products/life_science_systems/science_imaging/arraygauge/
ArrayGauge [FUJIFILM]
Fujifilm ArrayGauge™ software is specifically designed for Macroarray and Microarray samples, with all the practical functions necessary for the most powerful array analysis.
Its ultra-friendly navigation and functions can handle any kind of array (CLONTECH, Genome Systems, Research Genetics - even hand-made arrays). It already includes virtually every contemporary cDNA membrane template on the market, with the flexibility to handle others as they develop.
ArrayGauge
Nandini Badarinarayan
FACS ( fluorescence-activated cell sorter)
PLPE
This package performs tests for paired high-throughput data.
http://bioconductor.org/packages/2.4/bioc/html/PLPE.html
Nandini Badarinarayan
'Rnw'
http://bioconductor.org/packages/2.4/bioc/html/ShortRead.html
Base classes, functions, and methods for representation of high-throughput, short-read sequencing data.
ShortRead
Nandini Badarinarayan
Probe Cell Analysis
Nandini Badarinarayan
Image analysis software
Jaguar
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/affylmGUI.html
A Graphical User Interface for affy analysis using the limma Microarray package
'affyImGUI'
Nandini Badarinarayan
'FDR'
http://spotfire.tibco.com/Products/Info.aspx
Spotfire’s interactive, visual capabilities for data analysis empower individuals to easily see trends, patterns outliers and unanticipated relationships in data with unprecedented speed and adaptability.
Spotfire
Nandini Badarinarayan
adSplit implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined.
Nandini Badarinarayan
Annotation-Driven Clustering
http://bioconductor.org/packages/2.4/bioc/html/adSplit.html
OMICS data
OLINgui
Graphical user interface for the OLIN package
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/OLINgui.html
Feature Extraction Software [Agilent Technologies]
Agilent Feature Extraction Software
Feature Extraction software
Nandini Badarinarayan
Feature Extraction Software
The software automatically finds and places microarray grids, rejects outlier pixels, accurately determines feature intensities and ratios, flags outlier pixels, and calculates statistical confidences. Application-specific QC reports summarize results and provide an at-a-glance quality assessment
http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/featureextractionsoftware/pages/default.aspx
gxl_format
data annotation objective
CBS algorithm
http://las.perkinelmer.com/Catalog/ProductInfoPage.htm?ProductID=7000060
ScanArray Express [PerkinElmer]
ScanArray Express
ScanArray Express provides superior spot finding and quantization algorithm. This combined with template adjustment features drives excellence in analysis performance.
ScanArray
Nandini Badarinarayan
Misclassification-Penalized Posteriors (MiPP)
KGML file
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/MergeMaid.html
The functions in this R extension are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be 'list','matrix', or 'ExpressionSet'. The main function is 'mergeExprs' which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function 'intcor' calculate the correlation coefficients. Other functions use the output from 'modelOutcome' to graphically display the results and cross-validate associations of gene expression data with survival.
MergeMaid
http://bioconductor.org/packages/2.4/bioc/html/Rredland.html
interface to redland RDF utilities
Rredland
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/vsn.html
The package implements a method for normalising microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references
vsn
Nandini Badarinarayan
A cluster based method for missing value estimationn is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided.
Nandini Badarinarayan
pcaMethods
http://bioconductor.org/packages/2.4/bioc/html/pcaMethods.html
MicroArraySuite 4.0
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/ArrayTools.html
'ArrayTools'
This package is designed to provide solutions for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays.
Nandini Badarinarayan
Imputation for microarray data (currently KNN only)
impute
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/impute.html
multivariate t mixture models
Clontech Laboratories, Inc
http://bioconductor.org/packages/2.4/bioc/html/weaver.html
This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included.
weaver
Nandini Badarinarayan
http://www.hitechtrader.com/detail.cfm?autonumber=64022
Applied Precision MicroArray Scanner Model arrayWoRx Comprehensive system that fully automates the image capture and quantitation of microarrays. by integrating Slid handling, fluorescent microscopy, and sophisticated spot scan and analysis software the systems detects and measures the fluorescence intensity at each of the specified elements in a microarray. The intensity data can be presented as image data, graphical representation, or as numerical data.
arrayWoRx
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/ROC.html
utilities for ROC, with uarray focus
ROC
Nandini Badarinarayan
RMA
A multiscan is an R package for combining multiple scans
http://bioconductor.org/packages/2.4/bioc/html/multiscan.html
multiscan
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/BioMVCClass.html
Creates classes used in model-view-controller (MVC) design
'BioMVCClass'
Nandini Badarinarayan
Nandini Badarinarayan
oligo
http://bioconductor.org/packages/2.4/bioc/html/oligo.html
A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level.
MWG Biotech
RMAExpress is a standalone GUI program for Windows (and Linux) to compute gene expression summary values for Affymetrix Genechip® data using the Robust Multichip Average expression summary and to carry out quality assessment using probe-level metrics. It does not require R nor is it dependent on any component of the BioConductor project. If focuses on processing 3' IVT expression arrays, exon and WT gene arrays.
http://rmaexpress.bmbolstad.com/
RMAExpress
Nandini Badarinarayan
Background adjustment using sequence information
http://bioconductor.org/packages/2.4/bioc/html/gcrma.html
Nandini Badarinarayan
'gcrma'
position weight matrix (PWM )
Agilent Technologies
http://www.bioinformatics.org/dchip/
Analysis and visualization of gene expression and SNP microarrays
dChip
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/GGtools.html
This package deals with hapmap SNP reports, GWAS, etc.
GGtools
Nandini Badarinarayan
http://dmaf.biochem.uci.edu/affymetrix_analysis_software.html
GeneSpring GX is a commercial software application that displays expression data in ways that help you conceptualize the information in your data
GeneSpring
Nandini Badarinarayan
Preprocessing of Agilent 4x44 array data
http://bioconductor.org/packages/2.4/bioc/html/Agi4x44PreProcess.html
'Agi4x44PreProcess'
Nandini Badarinarayan
GEO Matrix Series file
Xba.CQV and Xba.regions
Nandini Badarinarayan
'cosmoGUI'
http://bioconductor.org/packages/2.4/bioc/html/cosmoGUI.html
cosmoGUI allows the user to interactively define constraint sets that can be used by the cosmo package to supervise the search for shared motifs in a set of DNA sequences. The constraints can be either adapted from a set of commonly used templates or defined from scratch.
http://bioconductor.org/packages/2.4/bioc/html/microRNA.html
Nandini Badarinarayan
microRNA
Nandini Badarinarayan
Nandini Badarinarayan
RankProd
Rank Product method for identifying differentially expressed genes with application in meta-analysis
http://bioconductor.org/packages/2.4/bioc/html/RankProd.html
http://rss.acs.unt.edu/Rdoc/library/ffmanova/html/ffmanova.html
General linear modeling of fixed-effects models with multiple responses is performed. The function calculates 50-50 MANOVA p-values, ordinary univariate p-values and adjusted p-values using rotation testing.
50-50 MANOVA
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/bridge.html
The bridge package consists of several functions for testing for dierential expression among mul-
tiple samples
'bridge'
Nandini Badarinarayan
ARR
http://bioconductor.org/packages/2.4/bioc/html/AffyExpress.html
'AffyExpress'
Nandini Badarinarayan
The purpose of this package is to provide a comprehensive and easy-to-use tool for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.
Nandini Badarinarayan
LBE
http://bioconductor.org/packages/2.4/bioc/html/LBE.html
LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis.
http://bioconductor.org/packages/2.4/bioc/html/ppiStats.html
Tools for the analysis of protein interaction data.
ppiStats
Nandini Badarinarayan
Nandini Badarinarayan
SPIA
This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study.
http://bioconductor.org/packages/2.4/bioc/html/SPIA.html
Hubert’s gamma
information
Information is a statement about some entity.
James Malone
information artifact
Grid grinder
Nandini Badarinarayan
Nested Effects Models to reconstruct phenotypic hierarchies
nem
http://bioconductor.org/packages/2.4/bioc/html/nem.html
ImaGene4.1 software
Nandini Badarinarayan
This includes exhaustive enumeration, triple-based inference,pairwise heuristic, module based inference, greedy hillclimbing
Nested Effects Models
TIFF image
Probe level Locally moderated Weighted median-t (PLW) and Locally Moderated Weighted-t (LMW).
Nandini Badarinarayan
plw
http://bioconductor.org/packages/2.4/bioc/html/plw.html
LPEadj
Two options are added to the LPE algorithm. The original LPE method sets all variances below the max variance in the ordered distribution of variances to the maximum variance. in LPEadj this option is turned off by default. The second option is to use a variance adjustment based on sample size rather than pi/2. By default the LPEadj uses the sample size based variance adjustment.
http://bioconductor.org/packages/2.4/bioc/html/LPEadj.html
Nandini Badarinarayan
Affymetrix GCOS v1.2
Nandini Badarinarayan
COSE, France
http://bioconductor.org/packages/2.4/bioc/html/biocDatasets.html
Synthetic datasets to a) demonstrate the usage of bioconductor packages, b) write unit tests, while keeping dependencies and ressources usage minimal.
'biocDatasets'
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/SLqPCR.html
Nandini Badarinarayan
SLqPCR
Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH
differential expression analysis objective
Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
http://bioconductor.org/packages/2.4/bioc/html/spikeLI.html
spikeLI
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/DynDoc.html
A set of functions to create and interact with dynamic documents and vignettes.
'DynDoc'
Nandini Badarinarayan
PerkinElmer
GenePix Pro
Nandini Badarinarayan
Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4.
made4
http://bioconductor.org/packages/2.4/bioc/html/made4.html
Nandini Badarinarayan
Genepix Pro 4.0
GenePix Pro v4.0 scanning software
GenePix Pro 4.0
Nandini Badarinarayan
rank-invariant set normalization
http://www.oxfordjournals.org/nar/webserver/summary/825
Software for microarray image analysis.
GridGrinder
Nandini Badarinarayan
KS measures how biased the ranks of a subset of items are among the ranks of the entire set
Kolmogorov Smirnov rank-sum based algorithm
http://bioconductor.org/packages/2.4/bioc/html/keggorth.html
Test package for a pathway 'ontology'
keggorth
Nandini Badarinarayan
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/affyio.html
Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.
'affyio'
'betr'
It calculates the probability of dierential expression for each feature (gene) in a data set.
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/betr.html
http://bioconductor.org/packages/2.4/bioc/html/Icens.html
Many functions for computing the NPMLE for censored and truncated data.
Icens
Nandini Badarinarayan
genefilter
http://bioconductor.org/packages/2.4/bioc/html/genefilter.html
Some basic functions for filtering genes
Nandini Badarinarayan
hierarchical clustering
Molecular Devices
goProfiles
http://bioconductor.org/packages/2.4/bioc/html/goProfiles.html
The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'.
Nandini Badarinarayan
global test allows the unit of analysis of the microarray experiment to be shifted from the single gene level to the pathway level, where a ‘pathway’ may be any set of genes, e.g. chosen using the Gene Ontology database or from earlier experiments.
Global test
http://bioconductor.org/packages/2.4/bioc/html/fdrame.html
'fdrame'
Nandini Badarinarayan
This package contains two main functions. The first is fdr.ma which takes normalized expression data array, experimental design and computes adjusted p-values It returns the fdr adjusted p-values and plots, according to the methods described in (Reiner, Yekutieli and Benjamini 2002). The second, is fdr.gui() which creates a simple graphic user interface to access fdr.ma
XML
http://falkow.stanford.edu/whatwedo/software/software.html
Dynamically chooses cutoffs for grouping into present/divergent genes based on the shape of the distribution. More resistant to variation in hybridization data than CCACK.
GACK
Nandini Badarinarayan
f-test
ImageReader
Nandini Badarinarayan
gene expression dataset
Nandini Badarinarayan
preprocessCore
A library of core preprocessing routines
http://bioconductor.org/packages/2.4/bioc/html/preprocessCore.html
Molecular Neuroscience Core, Center for Behavioral Neuroscience, Atlanta
simpleaffy
http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html
Nandini Badarinarayan
Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures
http://bioconductor.org/packages/2.4/bioc/html/nudge.html
Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially expressed genes in the cases where the two samples are being compared directly or indirectly (via a common reference sample)
Nandini Badarinarayan
nudge
Nandini Badarinarayan
xps
Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
http://bioconductor.org/packages/2.4/bioc/html/xps.html
ArrayVision
Nandini Badarinarayan
Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed
http://bioconductor.org/packages/2.4/bioc/html/flowClust.html
'flowClust'
Nandini Badarinarayan
'cellHTS'
Analysis of cell-based RNA interference screens
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/cellHTS.html
LPE
http://bioconductor.org/packages/2.4/bioc/html/LPE.html
Nandini Badarinarayan
This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library.
The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values.
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/plier.html
plier
k-means
limma
Nandini Badarinarayan
Data analysis, linear models and differential expression for microarray data.
http://bioconductor.org/packages/2.4/bioc/html/limma.html
R interface to boost graph library algorithm (RBGL)
http://bioconductor.org/packages/2.4/bioc/html/yaqcaffy.html
Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.
yaqcaffy
Nandini Badarinarayan
'sproc'
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/Category.html
A collection of tools for performing category analysis.
'Category'
it is where we fit a model with probe level and chip level parameters on a probeset by probeset basis
'PLM'
k-cores
S-Score algorithm
This package creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object.
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/affyQCReport.html
'affyQCReport'
Affymetrix
http://bioconductor.org/packages/2.4/bioc/html/flowCore.html
This package provides S4 data structures and basic functions to deal with flow cytometry data.
'flowCore'
Nandini Badarinarayan
Slides are scanned using CodeLink Expression Scanning Software
CodeLink Expression Scanning Software
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/flowQ.html
This package provides quality control and quality assessment tools for flow cytometry data.
'flowQ'
Nandini Badarinarayan
microarray data
http://bioconductor.org/packages/2.4/bioc/html/GeneticsBase.html
This package (GeneticsBase) provides a foundation of efficient data structures and easy-to-use manipulation functions.
GeneticsBase
Nandini Badarinarayan
mas5 format
Processing Mass Spectrometry spectrum by using wavelet based algorithm
MassSpecWavelet
http://bioconductor.org/packages/2.4/bioc/html/MassSpecWavelet.html
Nandini Badarinarayan
A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
IAO
programming language
GenePix [Axon Instruments]
GenePix
Nandini Badarinarayan
An interactive tool to visualize long vectors of integer data by means of Hilbert curves
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/HilbertVisGUI.html
HilbertVisGUI
Nandini Badarinarayan
Functions and classes for DNA copy number profiling of array-CGH data
http://bioconductor.org/packages/2.4/bioc/html/SMAP.html
SMAP
A DFP version of a FP (fuzzy pattern) only includes those genes that can serve to differentiate it from the rest of the patterns.This algorithm is based on the discretization of float values (gene expression values) stored in an ExpressionSet object into labels combining 'Low', 'Medium' and 'High'
Discriminant Fuzzy Pattern Algorithm
http://bioconductor.org/packages/2.4/bioc/html/rMAT.html
R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.
Nandini Badarinarayan
rMAT
http://bioconductor.org/packages/2.4/bioc/html/OLIN.html
Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data
OLIN
Nandini Badarinarayan
MAVI Pro
Nandini Badarinarayan
http://www.bio-medicine.org/
Acuity is the complete enterprise microarray informatics platform for microarray data storage, data filtering and data analysis. It analysis tools for quality, visualizations for discovery and Data Management for Security.
Acuity
Nandini Badarinarayan
http://www.silicongenetics.com/cgi/SiG.cgi/Support/gs_r_int.smf
SiliconGenetics GeneSpring
The GeneSpring-R integration package will allow you to expand the capability of GeneSpring by integrating R programs seamlessly into GeneSpring. With the integration package you will be able to use the power of R and BioConductor scripts in GeneSpring's rich graphical environment
Silicon Genetics Genespring
Nandini Badarinarayan
Locally Moderated Weighted-t (LMW) method
'BPMAP'
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/vbmp.html
vbmp
Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination.
Heterogeneous Error Model (HEM)
HaarSeg algorithm
Feature Extraction Software
Nandini Badarinarayan
MAS 5.0 software
MicroArraySuite 5.0
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/apComplex.html
'apComplex'
Nandini Badarinarayan
This package functions to estimate a bipartite graph of protein complex membership using AP-MS data.
DFW
http://bioconductor.org/packages/2.4/bioc/html/GeneSelector.html
The term 'GeneSelector' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list in various featured ranking methods (currently 15). In addition, the stability of the findings can be taken in account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise.
GeneSelector
Nandini Badarinarayan
Logit-t algorithm
http://www.chem.agilent.com/en-US/products/instruments/lab-on-a-chip/2100expertsoftware/pages/default.aspx
Exper 2100 offers powerful data evaluation tools for all available assays, automatic and manual integration, smear analysis and many assay-specific tools.
Expert 2100
Nandini Badarinarayan
'aroma.light'
Nandini Badarinarayan
This package functions as methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.
http://bioconductor.org/packages/2.4/bioc/html/aroma.light.html
GEO data type
CHP file
Paired t-test , Paired L-statistic and Paired Lw-statistic with their FDRs
statistical tests
EMBL
http://bioconductor.org/packages/2.4/bioc/html/hopach.html
The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering).
Nandini Badarinarayan
hopach
'bimap object'
Functions and data used in Balasubramanian, et al. (2004)
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/GraphAT.html
GraphAT
We propose importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments.
MANOR
http://bioconductor.org/packages/2.4/bioc/html/MANOR.html
Nandini Badarinarayan
'heatmaps'
clustered data set
Nandini Badarinarayan
This package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. This library provides a graphical interface allowing QC, filtering, statistical validation, and alternative splicing analysis.
http://bioconductor.org/packages/2.4/bioc/html/oneChannelGUI.html
oneChannelGUI
Data is an information entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
IAO
data
http://bioconductor.org/packages/2.4/bioc/html/tkWidgets.html
Widgets to provide user interfaces. tcltk should have been installed for the widgets to run.
tkWidgets
Nandini Badarinarayan
Functions to computationally simulate the AP-MS technology based on wet-lab data.
Nandini Badarinarayan
simulatorAPMS
http://bioconductor.org/packages/2.4/bioc/html/simulatorAPMS.html
'FASTA'
'gct'
Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously.
http://bioconductor.org/packages/2.4/bioc/html/RpsiXML.html
RpsiXML
Nandini Badarinarayan
http://smd.stanford.edu/resources/restech.shtml
Processes fluorescent images of microarrays
ScanAlyze
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/RBGL.html
Nandini Badarinarayan
A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.
RBGL
A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.
http://bioconductor.org/packages/2.4/bioc/html/affyPLM.html
Nandini Badarinarayan
'affyPLM'
SDF format
.rma format
quantile normalization
Biometric Research Branch
Logic regression
Concordance
Axon GenePix Pro 3
Nandini Badarinarayan
http://dmaf.biochem.uci.edu/affymetrix_analysis_software.html
Tiling Analysis Software (TAS) is a freely downloadable tool for analysis, with which one can perform a simulation to assess the likelihood that an observed probe overlap region is different from the expected overlap with no enrichment from binding, and can derive an interval overlap report and/or computation of summary statistics.
TAS Software
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/GeneRfold.html
Package manipulating sequences with fold routines
GeneRfold
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/snapCGH.html
Methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays.
Nandini Badarinarayan
snapCGH
Matforsk
logicFS
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/logicFS.html
Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification.
http://bioconductor.org/packages/2.4/bioc/html/arrayQuality.html
This package functions for performing print-run and array level quality assessment.
'arrayQuality'
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/GGBase.html
This package is an infrastructure for dealing with hapmap SNP reports, GWAS, etc.
GGBase
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/geneplotter.html
Some basic functions for plotting genetic data
geneplotter
Nandini Badarinarayan
http://hmg.oxfordjournals.org/cgi/reprint/12/17/2145.pdf
Microarray image quantification is performed using GLEAMS software
GLEAMS software
Nandini Badarinarayan
Bio-Rad Laboratories, Inc.
Queries and data structures for protein interactions
Nandini Badarinarayan
Rintact
http://bioconductor.org/packages/2.4/bioc/html/Rintact.html
Nandini Badarinarayan
'fbat'
http://bioconductor.org/packages/2.4/bioc/html/fbat.html
This package implements a broad class of Family Based Association Tests for genetids data, with adjustments for population admixture using the code from the 'FBAT' software program
QuantArray, PackaardBiochip technologies
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/annotate.html
Using R enviroments for annotation.
'annotate'
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/xcms.html
Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, and mzData files. Preprocesses data for high-throughput, untargeted analyte profiling.
xcms
Nandini Badarinarayan
Bootstrap
Research Genetics
http://linus.nci.nih.gov/BRB-ArrayTools.html
BRB-ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data. It was developed by professional statisticians experienced in the analysis of microarray data and involved in the development of improved methods for the design and analysis of microarray based experiments. The system incorporates a variety of powerful analytic and visualization tools developed specifically for microarray data analysis.
BRB-ArrayTools
Nandini Badarinarayan
ArrayVision 6.0 (Imaging Research Inc.)
Nandini Badarinarayan
Nandini Badarinarayan
SAFE is a resampling-based method for testing functional categories is gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions.
3
http://bioconductor.org/packages/2.4/bioc/html/safe.html
safe
http://bioconductor.org/packages/2.4/bioc/html/Resourcerer.html
This package allows user either to read an annotation data file from TIGR Resourcerer as a matrix or convert the file into a Bioconductor annotation data package using the AnnBuilder package.
Resourcerer
Nandini Badarinarayan
Bioconductor
http://www.geneservice.co.uk/services/geneexpression/overview_1700.jsp
Microarrays are powerful tools for discovering levels of gene expression. Geneservice have invested in the latest gene expression microarray system from Applied Biosystems so that the widest choice of platform is available to our customers. The key features of this system are:
Sensitivity: a detection threshold of as little as a femtomole of expresseed mRNA and requiring as little as 500ng of starting total RNA.
Content: each probe is associated with a gene sequence buiult on unique Celera data and validated by public RefSeqs all of which have been curated.
Pipeline: complete integrated solutions for gene expression research including Applied Biosystems Bioinformatic tools and ready-to-go gene expression TaqMan assays for validation of results.
Applied Biosystems 1700 Expression Array System Software
Nandini Badarinarayan
Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or lost) to each chromosomal regions identified.
GLAD
http://bioconductor.org/packages/2.4/bioc/html/GLAD.html
Nandini Badarinarayan
'Bayesian Model'
Nandini Badarinarayan
The ABarray is designed to work with Applied Biosystems whole genome microarray platform, as well as any other platform whose data can be tranformed into expression data matrix.
http://www.bioconductor.org/packages/2.4/bioc/html/ABarray.html
ABarray
data visualization objective
UC Irvine
'CDF'
http://bioconductor.org/packages/2.4/bioc/html/panp.html
panp
Nandini Badarinarayan
A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.
Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)
http://bioconductor.org/packages/2.4/bioc/html/Mfuzz.html
Nandini Badarinarayan
Mfuzz
http://www.findownersearch.com/optiquant/7766418/
Computer software for image acquisition, analysis and reporting, for use in the life sciences
Optiquant
Nandini Badarinarayan
A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/ITALICS.html
ITALICS
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