classified
0.3
Nandini Badarinarayan
James Malone
Helen Parkinson
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/quantsmooth.html
Quantile smoothing and genomic visualization of array data
quantsmooth
Analysing data
multinomial probit regression with Gaussian Process priors
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.
http://bioconductor.org/packages/2.4/bioc/html/GEOquery.html
Nandini Badarinarayan
GEOquery
Paired t-test , Paired L-statistic and Paired Lw-statistic with their FDRs
statistical tests
ANNOVA
'ANOVA'
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
SBMLR file
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.
Package manipulating nucleotidic sequences (Embl, Fasta, GenBank)
http://bioconductor.org/packages/2.4/bioc/html/GeneR.html
Nandini Badarinarayan
GeneR
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
Gene Recommender algorithm
gmt format
The Rosetta ResolverĀ® 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.
http://www.rosettabio.com/products/resolver
Nandini Badarinarayan
Rosetta Resolver
avgNRRs
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
Robust likelihood-based survival modeling
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
FoxDimmicT
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
http://bioconductor.org/packages/2.4/bioc/html/GeneRegionScan.html
Nandini Badarinarayan
GeneRegionScan
'Smith-Waterman'
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
Technological Advances for Genomics and Clinics, France
GenePix 4100A [Axon Instruments]
Nandini Badarinarayan
GenePix 4100A
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
Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
http://bioconductor.org/packages/2.4/bioc/html/spikeLI.html
spikeLI
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
Convenience data structures and functions to handle cdfenvs
http://www.bioconductor.org/packages/release/Software.html
Nandini Badarinarayan
'altcdfenvs'
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.
http://bioconductor.org/packages/2.4/bioc/html/GEOmetadb.html
Nandini Badarinarayan
GEOmetadb
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
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
hypergeometric enrichment
Nandini Badarinarayan
GenePix 3.0.6
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
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.
Axon GenePix Pro
Nandini Badarinarayan
GenePix Pro [Axon Instruments]
two-stage measurement error model
SBML file
associative T method
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
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.
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
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.
'Rnw'
'plots'
'M-estimation regression'
Similarity score
AMDIS
Nandini Badarinarayan
GenePix 4.1
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
algorithm
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/ssize.html
Functions for computing and displaying sample size information for gene expression arrays.
ssize
Nandini Badarinarayan
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.
http://www.moleculardevices.com/pages/software/gn_genepix_pro.html
Nandini Badarinarayan
Gene Pix
Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, EIC correlation based tagging of unknown adducts and fragments
Nandini Badarinarayan
'CAMERA'
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
http://bioconductor.org/packages/2.4/bioc/html/vsn.html
Nandini Badarinarayan
vsn
A package for plotting genomic data by chromosomal location
http://bioconductor.org/packages/2.4/bioc/html/idiogram.html
Nandini Badarinarayan
idiogram
Bahler Lab
GEO Matrix Series files
quantile normalization
Using R enviroments for annotation.
http://bioconductor.org/packages/2.4/bioc/html/annotate.html
Nandini Badarinarayan
'annotate'
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.
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 āpathwayā may be any set of genes, e.g. chosen using the Gene Ontology database or from earlier experiments.
Global test
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.
http://www.hitechtrader.com/detail.cfm?autonumber=64022
Nandini Badarinarayan
arrayWoRx
k-nearest neighbour classification
This package contains class definitions, validity checks, and initialization methods for classes used by the oligo package.
http://bioconductor.org/packages/2.4/bioc/html/oligoClasses.html
Nandini Badarinarayan
oligoClasses
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.
'png'
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
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
http://www.silicongenetics.com/cgi/SiG.cgi/Support/gs_r_int.smf
Nandini Badarinarayan
Silicon Genetics Genespring
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.
http://purl.obolibrary.org/obo/IAO_0000010
Nandini Badarinarayan
James Malone
Helen Parkinson
Tomasz Adamusiak
software
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
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
A set of tools to work with alternative splicing
Nandini Badarinarayan
splicegear
http://bioconductor.org/packages/2.4/bioc/html/splicegear.html
Nandini Badarinarayan
Reverse engineering of molecular regulatory networks with qp-graphs
http://bioconductor.org/packages/2.4/bioc/html/qpgraph.html
qpgraph
Support for Springer monograph on Bioconductor
http://bioconductor.org/packages/2.4/bioc/html/RbcBook1.html
Nandini Badarinarayan
RbcBook1
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
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
http://bioconductor.org/packages/2.4/bioc/html/TypeInfo.html
Nandini Badarinarayan
TypeInfo
ALL/AML data set
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
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
This package contains an implementation of the S-Score algorithm
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/sscore.html
sscore
Genedata ExpressionistĀ® is an enterprise solution that integrates, stores and analyzes transcriptomics, proteomics and metabolomics data as well as a wide variety of phenotypic data.
http://www.genedata.com/products/expressionist/overview.html
Nandini Badarinarayan
GeneData Expressionist Analyst v4.0.5
quantile regression techniques
GEO_data type
mrnet algorithm
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.
http://tagc.univ-mrs.fr/bioinformatics/bzscan/
Nandini Badarinarayan
BZScan
Many functions for computing the NPMLE for censored and truncated data.
http://bioconductor.org/packages/2.4/bioc/html/Icens.html
Nandini Badarinarayan
Icens
This package functions for handling data from Bioconductor Affymetrix annotation data packages.Allows searching biological metadata using various criteria.
http://bioconductor.org/packages/2.4/bioc/html/annaffy.html
Nandini Badarinarayan
'annaffy'
Nandini Badarinarayan
arrayWoRx 2.0
position weight matrix (PWM )
k-means
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.
Nandini Badarinarayan
yaqcaffy
visualization of data
Signaling Pathway Impact Analysis (SPIA) algorithm
This package generates a quality metrics report on ExpressionSet, NChannelSet, AffyBatch or BeadLevelList objects containing microarray data with one or two channels.
http://bioconductor.org/packages/2.4/bioc/html/arrayQualityMetrics.html
Nandini Badarinarayan
'arrayQualityMetrics'
Queries and data structures for protein interactions
Nandini Badarinarayan
Rintact
http://bioconductor.org/packages/2.4/bioc/html/Rintact.html
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.
http://www.baymedia.com/gemtools/
Nandini Badarinarayan
GEMTools 2.4
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
Raytest
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.
http://bin.tugraz.at/Tools/ArrayNorm.html
Nandini Badarinarayan
ArrayNorm
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.
Theodore Tsāoās
average log expression across arrays (ALE)
Bayesian models for differential gene expression
http://bioconductor.org/packages/2.4/bioc/html/BGmix.html
Nandini Badarinarayan
'BGmix'
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.
k-cores
RMA
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).
http://www.rubion.rub.de/labor/pdf/BASREAD.pdf
Nandini Badarinarayan
BasReader 3.01
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
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
'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).
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.
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
Categorized views of R package repositories
http://bioconductor.org/packages/2.4/bioc/html/biocViews.html
Nandini Badarinarayan
'biocViews'
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
'gene_expression'
GC-RMA Quantification (Stratagene ArrayAssist Expression Software)
Single-user desktop software package for analyzing microarray data from multiple microarray platforms.
http://www.biocompare.com/ProductDetails/475470/ArrayAssist-Expression-Software-(1-year-academic-license).html
Nandini Badarinarayan
GC-RMA Quantification
ScanArray version 3.1
Nandini Badarinarayan
ScanArray v3.1 software
qPCR data
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
Nandini Badarinarayan
Multivariate correlation estimation and statistical inference.
'CORREP'
http://bioconductor.org/packages/2.4/bioc/html/CORREP.html
R data frame
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
Nandini Badarinarayan
2
Nandini Badarinarayan
A package that implements some simple graph handling capabilities.
graph
http://bioconductor.org/packages/2.4/bioc/html/graph.html
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
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
tilingArray
http://bioconductor.org/packages/2.4/bioc/html/tilingArray.html
Transcript mapping with high-density oligonucleotide tiling arrays
Nandini Badarinarayan
'jpeg'
Xba.CQV and Xba.regions
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
BaldiLongT
annotate data
Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see
Nandini Badarinarayan
'affycoretools'
http://bioconductor.org/packages/2.4/bioc/html/affycoretools.html
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.
This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included.
http://bioconductor.org/packages/2.4/bioc/html/weaver.html
Nandini Badarinarayan
weaver
'pdf'
'MAS5'
'heatmaps'
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
TIGR Spotfinder was designed for the rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression
http://www.tm4.org/contributors.html
Nandini Badarinarayan
Spotfinder [TIGR]
This package provides examples and code that make use of the different graph related packages produced by Bioconductor.
http://bioconductor.org/packages/2.4/bioc/html/biocGraph.html
Nandini Badarinarayan
'biocGraph'
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.
COSE, France
GASSCO method
gene array analysis algorithm
gpr format
This package deals with hapmap SNP reports, GWAS, etc.
http://bioconductor.org/packages/2.4/bioc/html/GGtools.html
Nandini Badarinarayan
GGtools
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
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
UC Irvine
Nandini Badarinarayan
GMS
'BED file'
XML
.java file
't-test'
BeadStudio Software is a modular analysis tool for genotyping, gene expression, and methylation applications
http://www.illumina.com/pages.ilmn?ID=35
Nandini Badarinarayan
Beadstudio
'HTML report'
multivariate t mixture models
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
http://bioconductor.org/packages/2.4/bioc/html/xcms.html
Nandini Badarinarayan
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.
http://falkow.stanford.edu/whatwedo/software/software.html
Nandini Badarinarayan
GACK
genefilter
http://bioconductor.org/packages/2.4/bioc/html/genefilter.html
Some basic functions for filtering genes
Nandini Badarinarayan
chi-square
Nandini Badarinarayan
Spot quantification
mas5 format
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
iterative local regression and model selection
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.
http://bioconductor.org/packages/2.4/bioc/html/snpMatrix.html
snpMatrix
Implements classes and methods for large-scale SNP association studies
Nandini Badarinarayan
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
Microarray image quantification is performed using GLEAMS software
http://hmg.oxfordjournals.org/cgi/reprint/12/17/2145.pdf
Nandini Badarinarayan
GLEAMS software
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
Analysis Software for Integrated Image Analysis for Spot Detection , Position and Quantification
http://www.cose.fr/us_dots.html
Nandini Badarinarayan
XDotsReader
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'
Stepwise normalization functions for cDNA microarray data.
http://bioconductor.org/packages/2.4/bioc/html/stepNorm.html
Nandini Badarinarayan
stepNorm
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.
http://bioconductor.org/packages/2.4/bioc/html/beadarray.html
Nandini Badarinarayan
'beadarray'
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
'Bayesian Model'
annotation data packages
This packages contains tools to support the construction of tcltk widgets
http://bioconductor.org/packages/2.4/bioc/html/widgetTools.html
Nandini Badarinarayan
widgetTools
gene expression dataset
hierarchical clustering
Fujifilm
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.
http://bioconductor.org/packages/2.4/bioc/html/biomaRt.html
Nandini Badarinarayan
'biomaRT'
OMICS data
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'
Logit-t algorithm
Speed Berkeley Research Group
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
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.
http://bioconductor.org/packages/2.4/bioc/html/matchprobes.html
Nandini Badarinarayan
matchprobes
modied version of the GLAD algorithm (Gain and Loss Analysis of DNA)
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
clustered data set
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
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
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
http://bioconductor.org/packages/2.4/bioc/html/GenomeGraphs.html
GenomeGraphs
Nandini Badarinarayan
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.
class discovery objective
R language
Technique which predicts a given transcription factor activity and then uses this infor- mation to predict its targets.
Hidden Variable Dynamic Modelling HVDM)
Nandini Badarinarayan
RMAExpress quantification
'cls'
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).
SLGI
http://bioconductor.org/packages/2.4/bioc/html/SLGI.html
Nandini Badarinarayan
A variety of data files and functions for the analysis of genetic interactions
rank product non-parametric method
Nandini Badarinarayan
'flowUtils'
This package provides utilities for flow cytometry data.
http://bioconductor.org/packages/2.4/bioc/html/flowUtils.html
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
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.
https://carmaweb.genome.tugraz.at/carma/
Nandini Badarinarayan
CARMAweb
NIH
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.
http://www.cambridgebluegnome.com/bluefuse.htm
Nandini Badarinarayan
BlueFuse
Provides plotting capabilities for R graph objects
http://bioconductor.org/packages/2.4/bioc/html/Rgraphviz.html
Nandini Badarinarayan
Rgraphviz
Nandini Badarinarayan
QuantArray, PackaardBiochip technologies
Bayesian integrated analysis of Affymetrix GeneChips
http://bioconductor.org/packages/2.4/bioc/html/bgx.html
Nandini Badarinarayan
'bgx'
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
Uniform interfaces to machine learning code for data in Bioconductor containers
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/MLInterfaces.html
MLInterfaces
Expression Consoleā¢ software supports probe set summarization and CHP file generation for 3' expression (e.g., GeneChipĀ® Human Genome U133 Plus 2.0 Array), gene-level (e.g., GeneChipĀ® Human Gene 1.0 ST array) and exon-level arrays (e.g., GeneChipĀ® 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/
center calculation objective
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.
http://bioconductor.org/packages/2.4/bioc/html/Ruuid.html
Ruuid
Nandini Badarinarayan
A package to provide UUID values in R
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.
gene list
ScISI
http://bioconductor.org/packages/2.4/bioc/html/ScISI.html
Package to create In Silico Interactomes
Nandini Badarinarayan
class prediction objective
Imputation for microarray data (currently KNN only)
impute
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/impute.html
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
chamber slide format
logicFS dataset
Nandini Badarinarayan
RMAExpress 2.0
Category analysis
Provides visualization tools for flow cytometry data
http://bioconductor.org/packages/2.4/bioc/html/flowViz.html
Nandini Badarinarayan
'flowViz'
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
rank-invariant set normalization
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
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.
http://bioconductor.org/packages/2.4/bioc/html/BufferedMatrix.html
Nandini Badarinarayan
'BufferedMatrix'
Motorola Life Sciences
BGAfun is a method to identify specifity determining residues in protein families
http://bioconductor.org/packages/2.4/bioc/html/bgafun.html
Nandini Badarinarayan
'bgafun'
Resampling-based multiple hypothesis testing
http://bioconductor.org/packages/2.4/bioc/html/multtest.html
multtest
Nandini Badarinarayan
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.
http://bioconductor.org/packages/2.4/bioc/html/Resourcerer.html
Nandini Badarinarayan
Resourcerer
mutual information matrix (MIM)
sim method
meta data
'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.
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/CGHregions.html
Dimension Reduction for Array CGH Data with Minimal Information Loss
'CGHregions'
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
RMAExpress is a standalone GUI program for Windows (and Linux) to compute gene expression summary values for Affymetrix GenechipĀ® 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
Basic class definitions and generics for external pointer based vector objects for R. A simple in-memory implementation is also provided
http://bioconductor.org/packages/2.4/bioc/html/externalVector.html
Nandini Badarinarayan
'externalVector'
sigPathway
Conducts pathway analysis by calculating the NT_k and NE_k statistics
http://bioconductor.org/packages/2.4/bioc/html/sigPathway.html
Nandini Badarinarayan
'images'
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
S-Score algorithm
SDF format
curve fitting objective
This algorithm offers improved confidence scores, quality scores for SNPās and batches, higher accuracy on different datasets and better performance.
CRLMM algorithm
Processes fluorescent images of microarrays
http://smd.stanford.edu/resources/restech.shtml
Nandini Badarinarayan
ScanAlyze
Hidden Markov Model
PLPE
This package performs tests for paired high-throughput data.
http://bioconductor.org/packages/2.4/bioc/html/PLPE.html
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
gxl_format
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/rbsurv.html
This package selects genes associated with survival.
rbsurv
makePlatformDesign creates the Platform Design environments (PDenvs) required by oligo.
http://bioconductor.org/packages/2.4/bioc/html/makePlatformDesign.html
Nandini Badarinarayan
makePlatformDesign
Synthetic datasets to a) demonstrate the usage of bioconductor packages, b) write unit tests, while keeping dependencies and ressources usage minimal.
http://bioconductor.org/packages/2.4/bioc/html/biocDatasets.html
Nandini Badarinarayan
'biocDatasets'
Biometric Research Branch
negative binomial distribution
rda
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
MAS
Affymetrix MicroArraySuite
AffymetrixĀ® Microarray Suite (MAS) is the core software product in the Affymetrix Software System providing instrument control, data acquisition, and data analysis for the entire GeneChipĀ® platform.
http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf
Nandini Badarinarayan
MIcroarray Analysis Suite
This includes exhaustive enumeration, triple-based inference,pairwise heuristic, module based inference, greedy hillclimbing
Nested Effects Models
CHP files
Analysis of cell-based RNA interference screens
Nandini Badarinarayan
'cellHTS2'
http://bioconductor.org/packages/2.4/bioc/html/cellHTS2.html
'MI'
RMA++
f-test
Serial Analysis of Gene Expression (SAGE)
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
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.
http://las.perkinelmer.com/Catalog/ProductInfoPage.htm?ProductID=7000060
Nandini Badarinarayan
ScanArray
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm
http://bioconductor.org/packages/2.4/bioc/html/SIM.html
Nandini Badarinarayan
SIM
Finds associations between DNA copy number and gene expression.
Continuous Wavelet Transform (CWT)-based peak detection algorithm
Functions and data used in Balasubramanian, et al. (2004)
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/GraphAT.html
GraphAT
data normalization objective
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.
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.
http://bioconductor.org/packages/2.4/bioc/html/makecdfenv.html
Nandini Badarinarayan
makecdfenv
.raw files
it is where we fit a model with probe level and chip level parameters on a probeset by probeset basis
'PLM'
Radial basis function
Processing Mass Spectrometry spectrum by using wavelet based algorithm
MassSpecWavelet
http://bioconductor.org/packages/2.4/bioc/html/MassSpecWavelet.html
Nandini Badarinarayan
Nandini Badarinarayan
QuantArray version 2
This package provides quality control and quality assessment tools for flow cytometry data.
http://bioconductor.org/packages/2.4/bioc/html/flowQ.html
Nandini Badarinarayan
'flowQ'
'bimap object'
Nandini Badarinarayan
Nested Effects Models to reconstruct phenotypic hierarchies
nem
http://bioconductor.org/packages/2.4/bioc/html/nem.html
'MAQC data'
Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or set of sequences.
http://bioconductor.org/packages/2.4/bioc/html/Biostrings.html
Nandini Badarinarayan
'Biostrings'
Nandini Badarinarayan
Absolute Expression Analysis
'Needleman-Wunsch'
CLR algorithm
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.
Nandini Badarinarayan
AIDA
RMA+
'cellHTS'
Analysis of cell-based RNA interference screens
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/cellHTS.html
MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments
http://bioconductor.org/packages/2.4/bioc/html/MEDME.html
Nandini Badarinarayan
MEDME
background correction objective
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)
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
Nandini Badarinarayan
Probe Cell Analysis
GraphAlignment
Nandini Badarinarayan
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.
http://bioconductor.org/packages/2.4/bioc/html/GraphAlignment.html
This package functions for performing print-run and array level quality assessment.
http://bioconductor.org/packages/2.4/bioc/html/arrayQuality.html
Nandini Badarinarayan
'arrayQuality'
This package provides mechanisms for automatic function prototyping and exposure of R functionality in a web services environment.
http://bioconductor.org/packages/2.4/bioc/html/RWebServices.html
Nandini Badarinarayan
RWebServices
Nandini Badarinarayan
SAGx
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.
decision tree induction objective
Parametric Analysis of Gene Set Enrichment
http://bioconductor.org/packages/2.4/bioc/html/PGSEA.html
Nandini Badarinarayan
PGSEA
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.
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.
http://rss.acs.unt.edu/Rdoc/library/ffmanova/html/ffmanova.html
Nandini Badarinarayan
50-50 MANOVA
Iteratively ReWeighted Least Squares
Nandini Badarinarayan
MicroArraySuite 4.0
CBS algorithm
cdt
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
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/microRNA.html
Nandini Badarinarayan
microRNA
Decomposition of Isotopic Patterns
http://bioconductor.org/packages/2.4/bioc/html/Rdisop.html
Nandini Badarinarayan
Rdisop
AWS algorithm
neural networks models
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
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
Nandini Badarinarayan
Statistical tools and data structures for analytic flow cytometry
http://bioconductor.org/packages/2.4/bioc/html/rflowcyt.html
rflowcyt
Mahalanobis distance
R interface to boost graph library algorithm (RBGL)
Power Law Global Error Model (PLGEM) analysis method
Generic database methods
http://bioconductor.org/packages/2.4/bioc/html/Rdbi.html
Nandini Badarinarayan
Rdbi
error correction objective
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
http://bioconductor.org/packages/2.4/bioc/html/arrayMvout.html
Nandini Badarinarayan
'arrayMvout'
Nandini Badarinarayan
ROC
http://bioconductor.org/packages/2.4/bioc/html/ROC.html
utilities for ROC, with uarray focus
SAM
PCpheno
http://bioconductor.org/packages/2.4/bioc/html/PCpheno.html
Nandini Badarinarayan
Tools to integrate, annotate, and link phenotypes to cellular organizational units such as protein complexes and pathways.
descriptive statistical calculation objective
mean calculation
2-sample pooled t-test
'CDF'
Misclassification-Penalized Posteriors (MiPP)
interface to redland RDF utilities
http://bioconductor.org/packages/2.4/bioc/html/Rredland.html
Nandini Badarinarayan
Rredland
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.
http://purl.obolibrary.org/obo/OBI_0000245
organization
Cambridge Bluegnome
microarray data
xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format.
http://bioconductor.org/packages/2.4/bioc/html/xmapbridge.html
Nandini Badarinarayan
xmapbridge
newick
ARR
Nonlinear Estimation by Iterative Partial Least Squares
Provides methods for accessing data stored in PostgreSQL tables.
http://bioconductor.org/packages/2.4/bioc/html/RdbiPgSQL.html
Nandini Badarinarayan
RdbiPgSQL
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
MWG Biotech
Bioconductor
A set of functions to dentify regional expression biases
Nandini Badarinarayan
reb
http://bioconductor.org/packages/2.4/bioc/html/reb.html
for the Support Vector Machine (SVM), as presented in [3] and the Nearest Shrunken Centroid (NSC)
Recursive Feature Elimination (RFE)
The package contains functions to perform the PDNN method described by Li Zhang et al.
http://bioconductor.org/packages/2.4/bioc/html/affypdnn.html
Nandini Badarinarayan
'affypdnn'
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/Category.html
A collection of tools for performing category analysis.
'Category'
Nandini Badarinarayan
Functions and classes for DNA copy number profiling of array-CGH data
SMAP
http://bioconductor.org/packages/2.4/bioc/html/SMAP.html
Pearson correlation estimator
QuantArray
QuantArrayĀ® is a powerful microarray analysis software that enables researchers to
easily and accurately visualize and quantitate gene expression data.
http://las.perkinelmer.com/content/relatedmaterials/brochures/bro_quantarray.pdf
Nandini Badarinarayan
QuantArray scanner software
Statistical Analysis with a number of procedures, providing statistical information such as analysis of variance, regression, multivariate analysis, and categorical data analysis.
http://en.wikipedia.org/wiki/SAS_System
Nandini Badarinarayan
SAS/STAT Software, Version 8
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
'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
differential expression analysis objective
Genepix Pro 4.0
GenePix Pro v4.0 scanning software
Nandini Badarinarayan
GenePix Pro 4.0
objective specification
The bridge package consists of several functions for testing for dierential expression among mul-
tiple samples
http://bioconductor.org/packages/2.4/bioc/html/bridge.html
Nandini Badarinarayan
'bridge'
OLINgui
Graphical user interface for the OLIN package
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/OLINgui.html
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
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'
SAS Institute Inc.
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
Estimation of local false discovery rate
http://bioconductor.org/packages/2.4/bioc/html/twilight.html
twilight
Nandini Badarinarayan
'CEL'
Functions that are needed by many other packages or which replace R functions
http://bioconductor.org/packages/2.4/bioc/html/Biobase.html
Nandini Badarinarayan
'Biobase'
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
ARACNE algorithm
MVCClass
Creates classes used in model-view-controller (MVC) design
http://bioconductor.org/packages/2.4/bioc/html/MVCClass.html
Nandini Badarinarayan
'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
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/rsbml.html
R support for SBML, using libsbml
rsbml
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
Research Genetics
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'
Random effects model
SNPRMA algorithm
PLIER (Probe Logarithmic Error Intensity Estimate) method
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'
This package can be used to handle MAGEML documents in Bioconductor
http://bioconductor.org/packages/2.4/bioc/html/RMAGEML.html
Nandini Badarinarayan
RMAGEML
Molecular Devices
http://bioconductor.org/packages/2.4/bioc/html/PAnnBuilder.html
Processing annotation data from public data repositories and building annoation data packages.
Nandini Badarinarayan
PAnnBuilder
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.
programming language
averaging objective
Bootstrap
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
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/OLIN.html
Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data
OLIN
Nandini Badarinarayan
Rosetta Biosoftware
Mixed model equations
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
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.
2
http://www.bioconductor.org/packages/2.4/bioc/html/ABarray.html
ABarray
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
Contains functions and classes that are needed by arrayCGH packages.
Nandini Badarinarayan
'CGHbase'
http://bioconductor.org/packages/2.4/bioc/html/CGHbase.html
Software and data to support the case studies.
http://bioconductor.org/packages/2.4/bioc/html/BiocCaseStudies.html
Nandini Badarinarayan
'BiocCaseStudies'
.rma format
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.
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
'AP-MS data'
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
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
'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
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'
Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments.
http://www.stat.berkeley.edu/users/terry/zarray/Software/smacode.html
Nandini Badarinarayan
R software
rtracklayer
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/rtracklayer.html
R interface to genome browsers and their annotation tracks
Loess algorithm
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
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
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
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
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.
'KLD'
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
A package for processing protein mass spectrometry data.
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/PROcess.html
PROcess
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
http://bioconductor.org/packages/2.4/bioc/html/RLMM.html
Nandini Badarinarayan
RLMM
A Genotype Calling Algorithm for Affymetrix SNP Arrays
hexagon binning algorithm
Nandini Badarinarayan
Imagene v4.0
Software for microarray image analysis.
http://www.oxfordjournals.org/nar/webserver/summary/825
Nandini Badarinarayan
GridGrinder
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
Logic regression
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
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
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
Test package for a pathway 'ontology'
http://bioconductor.org/packages/2.4/bioc/html/keggorth.html
Nandini Badarinarayan
keggorth
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
Presence-Absence calls with Negative Probesets (PANP)
Nandini Badarinarayan
'flagme'
Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data
http://bioconductor.org/packages/2.4/bioc/html/flagme.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
Regression model
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
http://bioconductor.org/packages/2.4/bioc/html/pathRender.html
pathRender
build graphs from pathway databases, render them by Rgraphviz
Nandini Badarinarayan
Tools for analyzing Micro Array experiments
http://cran.r-project.org/web/packages/maanova/index.html
Nandini Badarinarayan
MAANOVA v1.2 package for MATLAB
Grid grinder
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
'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
Imagene
ImaGene [BioDiscovery]
ImaGene microarray image analysis software by biodiscovery for microarrays, protein arrays and CGH analysis.
http://www.biodiscovery.com/index/imagene
Nandini Badarinarayan
ImaGene
Nandini Badarinarayan
ICS-501 (version 2.3) Image Capture System
cross validation
Multivariate correlation estimator
Computer software for image acquisition, analysis and reporting, for use in the life sciences
http://www.findownersearch.com/optiquant/7766418/
Nandini Badarinarayan
Optiquant
'Markov Chain Monte Carlo'
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
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.
http://dmaf.biochem.uci.edu/affymetrix_analysis_software.html
Nandini Badarinarayan
Cyber-T
Genepix pro 3.0
Nandini Badarinarayan
GenePix Pro 3.0
F test
Median Average Difference Algorithm
'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
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).
http://maexplorer.sourceforge.net/MaeRefMan/hmaeDoc2.4.2.html
Nandini Badarinarayan
Pathways 2.01 software
'diffGeneAnalysis'
http://bioconductor.org/packages/2.4/bioc/html/diffGeneAnalysis.html
Nandini Badarinarayan
Analyze microarray data
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
Nandini Badarinarayan
ImageReader
Hypergeometric probability
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'
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/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
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.
PerkinElmer
This package provides S4 data structures and basic functions to deal with flow cytometry data.
http://bioconductor.org/packages/2.4/bioc/html/flowCore.html
Nandini Badarinarayan
'flowCore'
MAGE-ML files
'gct'
Nandini Badarinarayan
MAGE-TAB inputting software
Concordance
MATLAB
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
Matforsk
Locally Moderated Weighted-t (LMW) method
'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
Analysis and visualization of gene expression and SNP microarrays
http://www.bioinformatics.org/dchip/
Nandini Badarinarayan
dChip
Nandini Badarinarayan
Agilent Feature Extraction software version 7.1
EMBL
ArrayGauge [FUJIFILM]
Fujifilm ArrayGaugeā¢ 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.
http://www.fujifilm.com/products/life_science_systems/science_imaging/arraygauge/
Nandini Badarinarayan
ArrayGauge
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.
http://www.research.bidmc.harvard.edu/AcademicIT/ImageQuant.asp
Nandini Badarinarayan
ImageQuant
Background adjustment using sequence information
http://bioconductor.org/packages/2.4/bioc/html/gcrma.html
Nandini Badarinarayan
'gcrma'
Hubertās gamma
Incyte Genomics
text data set
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
This package contains functions useful for designing genetics studies, including power and sample-size calculations.
http://bioconductor.org/packages/2.4/bioc/html/GeneticsDesign.html
Nandini Badarinarayan
GeneticsDesign
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
limma
Nandini Badarinarayan
Data analysis, linear models and differential expression for microarray data.
http://bioconductor.org/packages/2.4/bioc/html/limma.html
Hardy-Weinberg equilibrium
comparing datasets
Nandini Badarinarayan
MAVI Pro
This package involves microarray Data related methods that utlize BufferedMatrix objects
http://bioconductor.org/packages/2.4/bioc/html/BufferedMatrixMethods.html
Nandini Badarinarayan
'BufferedMatrixMethods'
'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
Lognormal Normal Model
Langmuir Isotherm
'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
Empirical Bayes rule
Nandini Badarinarayan
ImaGene 3.0
MathWorks
Background adjustment using sequence information
http://www.bioconductor.org/packages/2.3/bioc/html/gcrma.html
Nandini Badarinarayan
gcRMA quantification
Bio Discovery
SVDimpute algorithm
Heterogeneous Error Model (HEM)
csv data set
These scripts are for primer design and initial microarray data processing and are available as .zip files:
http://www.bahlerlab.info/resources/
Nandini Badarinarayan
Initial microarray data processing (data filtering, local normalisation and quality control)
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.
This package (GeneticsBase) provides a foundation of efficient data structures and easy-to-use manipulation functions.
http://bioconductor.org/packages/2.4/bioc/html/GeneticsBase.html
Nandini Badarinarayan
GeneticsBase
HaarSeg algorithm
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.
Nandini Badarinarayan
A Graphical User Interface for the limma Microarray package
limmaGUI
http://bioconductor.org/packages/2.4/bioc/html/limmaGUI.html
data
Firth's bias reduction procedure
MAS 5.0 software
Nandini Badarinarayan
MicroArraySuite 5.0
Preprocessing of Agilent 4x44 array data
http://bioconductor.org/packages/2.4/bioc/html/Agi4x44PreProcess.html
'Agi4x44PreProcess'
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.
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
Nandini Badarinarayan
ImaGene4.1 software
Bio-Rad Laboratories, Inc.
Laplace mixture model
Exper 2100 offers powerful data evaluation tools for all available assays, automatic and manual integration, smear analysis and many assay-specific tools.
http://www.chem.agilent.com/en-US/products/instruments/lab-on-a-chip/2100expertsoftware/pages/default.aspx
Nandini Badarinarayan
Expert 2100
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
Molecular Neuroscience Core, Center for Behavioral Neuroscience, Atlanta
non-linear functional regression model with both additive and multiplicative error terms
non-linear functional regression model
Institute for Genomics and Bioinformatics Graz University of Technology
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/HEM.html
HEM
This package fits heterogeneous error models for analysis of microarray data
Sample size and power analysis for microarray data, where two groups are analysed.
SSPA
http://bioconductor.org/packages/2.4/bioc/html/SSPA.html
Nandini Badarinarayan
This package contains functions connecting R with the Gaggle
http://bioconductor.org/packages/2.4/bioc/html/gaggle.html
Nandini Badarinarayan
'gaggle'
Creates classes used in model-view-controller (MVC) design
http://bioconductor.org/packages/2.4/bioc/html/BioMVCClass.html
Nandini Badarinarayan
'BioMVCClass'
SBML model
Genicon Sciences
feature extraction
Nandini Badarinarayan
lapmix
http://bioconductor.org/packages/2.4/bioc/html/lapmix.html
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.
DFW
Nandini Badarinarayan
Agilent Feature Extraction 5.1.1
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
clustering algorithm
Fischer's Exact Test
Havard School of Public Health
MATLABĀ® 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
http://www.mathworks.com/products/matlab/?s_cid=SA_trafrefpai_MLipspot_Doc_bioinfo_MATLAB
Nandini Badarinarayan
MATLAB
Probe level Locally moderated Weighted median-t (PLW) method
FACS ( fluorescence-activated cell sorter)
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
http://bioconductor.org/packages/2.4/bioc/html/BicARE.html
Nandini Badarinarayan
'BicARE'
Library Search Algorithm
ILLUMINA data
Package manipulating sequences with fold routines
http://bioconductor.org/packages/2.4/bioc/html/GeneRfold.html
Nandini Badarinarayan
GeneRfold
Molecular Dynamics
Dynamic programming algorithm
J. Craig Venter Institute
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
Jaccardās index
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
Clontech Laboratories, Inc
Illumina
PPC algorithm
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
likelihood method
LC-MS data
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
digital gene expression (DGE) datasets
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
tools for working with ontologies and graphs
http://bioconductor.org/packages/2.4/bioc/html/ontoTools.html
Nandini Badarinarayan
ontoTools
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
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
Nandini Badarinarayan
Feature Extraction Software
Nandini Badarinarayan
Agilent Technologies Software
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
Dana-Farber Cancer Institute and Harvard School of Public Health
This package is an infrastructure for dealing with hapmap SNP reports, GWAS, etc.
http://bioconductor.org/packages/2.4/bioc/html/GGBase.html
Nandini Badarinarayan
GGBase
data file format
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.
http://blast.ncbi.nlm.nih.gov/Blast.cgi
Nandini Badarinarayan
BLAST
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'
Image analysis software
Nandini Badarinarayan
Jaguar
GenePix [Axon Instruments]
Nandini Badarinarayan
GenePix
This package provides user interface and database connection code for annotation data packages using SQLite data storage.
http://bioconductor.org/packages/2.4/bioc/html/AnnotationDbi.html
Nandini Badarinarayan
'AnnotationDbi'
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.
Gene selection based on a mixture of marginal distributions
GeneSelectMMD
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/GeneSelectMMD.html
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.
Nandini Badarinarayan
tkWidgets
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
'sproc'
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
log file
Fixed effect model
Wilcoxon
Nandini Badarinarayan
ArrayVision 6.0 (Imaging Research Inc.)
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
Gamma-Gamma hierarchical model
Computer software for the analysis and comparison of Atlasā¢ nylon and plastic arrays.
http://www.clontech.com/images/pacs/634650-PA27475.pdf
Nandini Badarinarayan
AtlasImage
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
pedigree data files
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
Gamma Gamma Model
A set of functions to create and interact with dynamic documents and vignettes.
http://bioconductor.org/packages/2.4/bioc/html/DynDoc.html
Nandini Badarinarayan
'DynDoc'
Some basic functions for plotting genetic data
http://bioconductor.org/packages/2.4/bioc/html/geneplotter.html
Nandini Badarinarayan
geneplotter
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
iterative Bayesian Model Averaging (BMA)
Multi sample aCGH analysis package using kernel convolution
http://bioconductor.org/packages/2.4/bioc/html/KCsmart.html
KCsmart
Nandini Badarinarayan
.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
'cosmo'
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.
Applied Biosystems
Nandini Badarinarayan
GenePix Pro
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.
Nandini Badarinarayan
Affymetrix Software
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
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.
http://bioconductor.org/packages/2.4/bioc/html/GeneSelector.html
Nandini Badarinarayan
GeneSelector
'sqlite'
Nandini Badarinarayan
Array_vision_(Interfocus)
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
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
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.
pair files
Linear modelling
'graphs'
Gaussian locally weighted regression
FC
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.
'BPMAP'
Nandini Badarinarayan
Tools for operation on genomic intervals.
genomeIntervals
http://bioconductor.org/packages/2.4/bioc/html/genomeIntervals.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.
http://bioconductor.org/packages/2.4/bioc/html/EBImage.html
Nandini Badarinarayan
'EBImage'
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.
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'
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
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.
http://www.geneservice.co.uk/services/geneexpression/overview_1700.jsp
Nandini Badarinarayan
Applied Biosystems 1700 Expression Array System Software
A package that provides a client interface to the KEGG SOAP server
http://bioconductor.org/packages/2.4/bioc/html/KEGGSOAP.html
Nandini Badarinarayan
KEGGSOAP
EBarrays provides tools for the analysis of replicated/unreplicated microarray data.
http://bioconductor.org/packages/2.4/bioc/html/EBarrays.html
'EBarrays'
Nandini Badarinarayan
design files
Base-Pair-Distance Kernel
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
information
Lognormal Normal with Modied Variance Model
Walter and Eliza Hall Institute
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 Microsoftā¢ Excel or database programs for flexibility in reporting.
Nandini Badarinarayan
ArrayVision
'explorase'
Nandini Badarinarayan
http://bioconductor.org/packages/2.4/bioc/html/explorase.html
This package explores and analyzes *omics data with R and GGobi
Set of functions and class definitions to be able to read and write GeneSpring specific data objects and covert them to BioConductor objects
http://bioconductor.org/packages/2.4/bioc/html/GeneSpring.html
Nandini Badarinarayan
GeneSpring
'lma'
Affymetrix
Gene-Set Enrichment Analysis
gtr
FCS
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
gff_format
GE Healthcare Life Sciences
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
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.
http://linus.nci.nih.gov/BRB-ArrayTools.html
Nandini Badarinarayan
BRB-ArrayTools
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
Applied Precision Life Science
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'
'dcf'
Expectation-Maximization(EM) algorithm
WilcEbam
'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
Nandini Badarinarayan
ArrayVision
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.
'FDR'
Define coerce methods for microarray data objects.
http://bioconductor.org/packages/2.4/bioc/html/convert.html
Nandini Badarinarayan
'convert'
Nandini Badarinarayan
GeneSpringGX
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
Nandini Badarinarayan
GenePix 5.0.1
local-pooled-error
Nandini Badarinarayan
Affymetrix GCOS v1.2
Stanford University
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
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
Nandini Badarinarayan
Agilent Feature Extraction software version 7.5
A multiscan is an R package for combining multiple scans
http://bioconductor.org/packages/2.4/bioc/html/multiscan.html
multiscan
Nandini Badarinarayan
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
http://bioconductor.org/packages/2.4/bioc/html/BSgenome.html
Nandini Badarinarayan
'BSgenome'
FARMS
University Of California, Berkeley
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
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.
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
http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/dnamicroarrayscanner/pages/default.aspx
Nandini Badarinarayan
Scanning software G2565AA version A6.3.1
Nandini Badarinarayan
Absolute Expression Analysis
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
https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600530
Nandini Badarinarayan
GeneTac Analyser
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.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=101854
Nandini Badarinarayan
CodeLink Expression Analysis Software
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).
Nandini Badarinarayan
GenePix Pro 6.0
Spotfireās interactive, visual capabilities for data analysis empower individuals to easily see trends, patterns outliers and unanticipated relationships in data with unprecedented speed and adaptability.
http://spotfire.tibco.com/Products/Info.aspx
Nandini Badarinarayan
Spotfire
KGML files
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.
http://dmaf.biochem.uci.edu/affymetrix_analysis_software.html
Nandini Badarinarayan
TAS Software
Nandini Badarinarayan
Agilent Feature Extraction software version A.5.1.1
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.
http://www.bio-medicine.org/
Nandini Badarinarayan
Acuity
Nandini Badarinarayan
ChipSkipper V0.99
variance-stabilizing transformation (VST) algorithm
'FASTA'
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
Base classes, functions, and methods for representation of high-throughput, short-read sequencing data.
http://bioconductor.org/packages/2.4/bioc/html/ShortRead.html
Nandini Badarinarayan
ShortRead
pamr
http://bioconductor.org/packages/2.4/bioc/html/pamr.html
Nandini Badarinarayan
Some functions for sample classification in microarrays
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
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
Complex Estimation Algorithm
Slides are scanned using CodeLink Expression Scanning Software
Nandini Badarinarayan
CodeLink Expression Scanning Software
http://bioconductor.org/packages/2.4/bioc/html/ppiStats.html
Tools for the analysis of protein interaction data.
Nandini Badarinarayan
ppiStats
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
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)
http://bioconductor.org/packages/2.4/bioc/html/GeneTraffic.html
Nandini Badarinarayan
GeneTraffic
Nandini Badarinarayan
GenePix Pro 6 [Axon Instruments]
Nandini Badarinarayan
The rama package consists of several functions for robust estimation of two color microarray intensities with replicates
2
rama
http://bioconductor.org/packages/2.4/bioc/html/rama.html
ChipSkipper [EMBL]
ChipSkipper Microarray Data Evaluation Software
ChipSkipper - an integrated tool for analysis, evaluation and quantitation of DNA micro-array data
http://angiogenesis.dkfz.de/software/chipskipper/index.htm
Nandini Badarinarayan
ChipSkipper
'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.
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
http://www.chem.agilent.com/
Nandini Badarinarayan
Agilent Scan Control
http://bioconductor.org/packages/2.4/bioc/html/pkgDepTools.html
pkgDepTools
Nandini Badarinarayan
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.
'parser'
TIBCO Software Inc
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.
http://purl.obolibrary.org/obo/IAO_0000129
James Malone
version number
Nandini Badarinarayan
Axon GenePix Pro 3
GeneSpring GX is a commercial software application that displays expression data in ways that help you conceptualize the information in your data
http://dmaf.biochem.uci.edu/affymetrix_analysis_software.html
Nandini Badarinarayan
GeneSpring
'ps'
Nandini Badarinarayan
GenePix Pro 3
create database
affyContam functions for structured corruption of cel file data to demonstrate QA effectiveness
http://bioconductor.org/packages/2.4/bioc/html/affyContam.html
Nandini Badarinarayan
'affyContam'
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
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.
http://www.bio-medicine.org/
Nandini Badarinarayan
ChipReader 3.1
Segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number
http://bioconductor.org/packages/2.4/bioc/html/DNAcopy.html
Nandini Badarinarayan
'DNAcopy'
TIFF image
Agilent Technologies
Functions to Analyze Microarray (Gene Expression) Data.
Nandini Badarinarayan
pickgene
http://bioconductor.org/packages/2.4/bioc/html/pickgene.html
FACS data
Nandini Badarinarayan
Scanning software
Routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics
http://bioconductor.org/packages/2.4/bioc/html/parody.html
Nandini Badarinarayan
parody
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
This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).
http://bioconductor.org/packages/2.4/bioc/html/GSEABase.html
Nandini Badarinarayan
GSEABase
Nandini Badarinarayan
preprocessCore
A library of core preprocessing routines
http://bioconductor.org/packages/2.4/bioc/html/preprocessCore.html
Genedata
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
GenePix Pro 5.0
Calculate distances
covdesc_file
http://bioconductor.org/packages/2.4/bioc/html/rHVDM.html
Hidden Variable Dynamic Modeling
Nandini Badarinarayan
rHVDM
A Graphical User Interface for affy analysis using the limma Microarray package
http://bioconductor.org/packages/2.4/bioc/html/affylmGUI.html
Nandini Badarinarayan
'affyImGUI'
has_specified_output
is_specified_input_of
has_legal_status
manufactures
achieves_planned_objective
c is_manufactured_by o means that there was a process p in which c was
built in which a person, or set of people or machines did the work(bore
the "Manufacturer Role", and those people/and or machines were members
or of directed by the organization to do this.
OBI
is_manufactured_by
is implemented in
is_specified_output_of
implements
has_specified_input
is about