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PackageDescriptionAuthorSoftwareRelease VersionDateCitation
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quantro http://www.bioconductor.org/packages/release/bioc/html/quantro.htmlA data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.Stehanie Hicks, Rafael IrizarryBioconductorBioconductor 3.012/1/2014
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MAnorm
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GeneGroupAnalysisR package providing functions to peform gene-set significance analysis over simple cross-sectional or time series data designs.Alejandro Quiroz-Zarate BioconductorBioconductor 2.10 (R 2.15)4/2/2012
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iBBiGIterative Binary Bi-clustering of Gene Sets. iBBiG is a bi-clustering algorithm which we apply to meta-gene set analysis of large numbers of gene expression datasets. The iterative algorithm extracts groups of phenotypes from multiple studies that are associated with similar gene setsDaniel Gusenleitner, Aedin CulhaneBioconductorBioconductor 2.10 (R 2.15)4/2/2012
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CancerMutationAnalysisCancer Mutation Analysis- implements gene and gene-set level analysis methods for somatic mutation studies of cancer. The gene-level methods distinguish between driver genes and passenger genes and incorporate a two-stage study designGiovanni Parmigiani, Simina M. Boca BioconductorBioconductor 2.10 (R 2.15)4/2/2012
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FFPEIdentify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).Levi WaldronBioconductorBioconductor 2.10 (R 2.15)4/2/2012
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ffpeExampleDataA subset of GSE17565 (April et al. 2009) containing 32 FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma, with a dilution series in technical duplicate.Levi WaldronBioconductorBioconductor 2.10 (R 2.15)4/2/2012
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pensimSimulation of continuous, correlated high-dimensional data with time to event or binary response, and parallelized functions for Lasso, Ridge, and Elastic Net penalized regression with repeated starts and two-dimensional tuning of the Elastic Net.Levi WaldronCRANR (≥ 2.10.0)2/23/2012
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RamiGOAmiGO visualize R interface. R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape.Markus Schroeder, Daniel Gusenleitner, Aedin Culhane, Benjamin Haibe-Kains, John Quackenbush BioconductorBioconductor 2.10 (R 2.15)4/2/2012
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PIPSGenerate Predicted Interval Plots. Simulate and plot confidence intervals of an effect estimate given observed data and a hypothesis about the distribution of future data.Daniel G. Muenz, Ray Griner, Huichao Chen, Lijuan Deng, Sachiko Miyahara, and Scott R. Evans, with contributions from Lingling Li, Hajime Uno, and Laura M. Smeaton.RR 2.152/12/2012
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RTopperThis package is designed to perform Gene Set Analysis across multiple genomic platformsLuigi Marchionni, Svitlana TyekuchevaBioconductorBioconductor 2.9 (R 2.14)11/1/2011
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ExomeCNVDetect CNV and LOH from Exome Sequecing DataJ. Fah Sathirapongsasuti, Hane Lee, and Stanley F. NelsonRR 2.1410/28/2011
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survC1Performs inference for C of risk prediction models with censored survival data, using the method proposed by Uno et al. (2011). Inference for the difference in C between two competing prediction models is also implemented.Hajime UnoRR 2.1410/2/2011
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survcompPerformance Assessment and Comparison for Survival AnalysisBenjamin Haibe-Kains, Markus Schroeder BioconductorBioconductor 2.8 (R 2.13)4/14/2011Schröder M, Culhane AC, Quackenbush J, Haibe-Kains B (2011) SurvComp: an R/Bioconductor package for performance assessment and comparison for survival analysis. Bioinformatics 27(22):3206-8
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genefuRelevant Functions for Gene Expression Analysis, Especially in Breast Cancer.Benjamin Haibe-Kains, Markus Schroeder BioconductorBioconductor 2.8 (R 2.13)4/14/2011Schröder M, Culhane AC, Quackenbush J, Haibe-Kains B (2011) SurvComp: an R/Bioconductor package for performance assessment and comparison for survival analysis. Bioinformatics 27(22):3206-8
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breastCancerMAINZ Gene expression dataset published by Schmidt et al. [2008] (MAINZ).Markus Schroeder, Benjamin Haibe-Kains Bioconductor (Experiment Data Package)Bioconductor 2.8 (R 2.13)4/14/2011Schröder M, Culhane AC, Quackenbush J, Haibe-Kains B (2011) SurvComp: an R/Bioconductor package for performance assessment and comparison for survival analysis. Bioinformatics 27(22):3206-8
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breastCancerNKI Genexpression dataset published by van't Veer et al. [2002] and van de Vijver et al. [2002] (NKI).Markus Schroeder, Benjamin Haibe-Kains Bioconductor (Experiment Data Package)Bioconductor 2.8 (R 2.13)4/14/2011Schröder M, Culhane AC, Quackenbush J, Haibe-Kains B (2011) SurvComp: an R/Bioconductor package for performance assessment and comparison for survival analysis. Bioinformatics 27(22):3206-8
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breastCancerTRANSBIG Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG).Markus Schroeder, Benjamin Haibe-Kains Bioconductor (Experiment Data Package)Bioconductor 2.8 (R 2.13)4/14/2011Schröder M, Culhane AC, Quackenbush J, Haibe-Kains B (2011) SurvComp: an R/Bioconductor package for performance assessment and comparison for survival analysis. Bioinformatics 27(22):3206-8
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breastCancerUNT Gene expression dataset published by Sotiriou et al. [2007] (UNT).Markus Schroeder, Benjamin Haibe-Kains Bioconductor (Experiment Data Package)Bioconductor 2.8 (R 2.13)4/14/2011Schröder M, Culhane AC, Quackenbush J, Haibe-Kains B (2011) SurvComp: an R/Bioconductor package for performance assessment and comparison for survival analysis. Bioinformatics 27(22):3206-8
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breastCancerUPPGene expression dataset published by Miller et al. [2005] (UPP).Markus Schroeder, Benjamin Haibe-Kains Bioconductor (Experiment Data Package)Bioconductor 2.8 (R 2.13)4/14/2011Schröder M, Culhane AC, Quackenbush J, Haibe-Kains B (2011) SurvComp: an R/Bioconductor package for performance assessment and comparison for survival analysis. Bioinformatics 27(22):3206-8
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breastCancerVDXGene expression datasets published by Wang et al. [2005] and Minn et al. [2007] (VDX).Markus Schroeder, Benjamin Haibe-Kains Bioconductor (Experiment Data Package)Bioconductor 2.8 (R 2.13)4/14/2011Schröder M, Culhane AC, Quackenbush J, Haibe-Kains B (2011) SurvComp: an R/Bioconductor package for performance assessment and comparison for survival analysis. Bioinformatics 27(22):3206-8
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attractMethods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor LandscapeJess MarBioconductorBioconductor 2.7 (R 2.12)10/18/2010
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betrIdentify differentially expressed genes in microarray time-course dataMartin Aryee BioconductorBioconductor 2.4 (R 2.9)4/21/2009
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made4Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4.Aedin CulhaneBioconductorBioconductor 1.6 or earlier (R 2.1)5/18/2005Culhane AC, Thioulouse J, Perriere G, Higgins DG.(2005) MADE4: an R package for multivariate analysis of gene expression data. Bioinformatics 21(11):2789-90.
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RankProdRank Product method for identifying differentially expressed genes with application in meta-analysisFangxin Hong BioconductorBioconductor 1.6 or earlier (R 2.1)5/18/2005
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Dept R Packages