Packages

379 packages on Bioconductor tagged VariantAnnotation or Bayesian or AffymetrixChip, most distinct IPs first

VariantAnnotation, Bayesian and AffymetrixChip in Topics

Package	Maintainer	Category	Latest version	Distinct IPs a month	Needs
limma Linear Models for Microarray and Omics DataGordon Smyth	Gordon Smyth	software	10 Aug 2026	44,656	6
DESeq2 Differential gene expression analysis based on the negative binomial distributionMichael Love	Michael Love	software	28 Apr 2026	31,845	54
edgeR Empirical Analysis of Digital Gene Expression Data in RYunshun Chen	Yunshun Chen	software	19 Oct 2026	31,065	10
VariantAnnotation Annotation of Genetic VariantsBioconductor Package Maintainer	Bioconductor Package Maintainer	software	28 Apr 2026	9,771	76
pcaMethods A collection of PCA methodsHenning Redestig	Henning Redestig	software	28 Apr 2026	7,214	10
hgu133plus2.db Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2)Bioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	3,923	43
Rsubread Mapping, quantification and variant analysis of sequencing dataWei Shi	Wei Shi	software	28 Apr 2026	2,722	8
ALDEx2 Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountGreg Gloor	Greg Gloor	software	28 Apr 2026	2,311	56
hgu133a.db Affymetrix Affymetrix HG-U133A Array annotation data (chip hgu133a)Bioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	1,818	43
hgu95av2.db Affymetrix Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2)Bioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	1,462	43
hgu133plus2cdf hgu133plus2cdfBioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	1,428	42
baySeq Empirical Bayesian analysis of patterns of differential expression in count dataSamuel Granjeaud	Samuel Granjeaud	software	28 Apr 2026	1,168	20
hugene10sttranscriptcluster.db Affymetrix hugene10 annotation data (chip hugene10sttranscriptcluster)Biocore Package Maintainer	Biocore Package Maintainer	annotation	no date on record	1,157	43
hgu95av2cdf hgu95av2cdfBioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	1,106	42
PureCN Copy number calling and SNV classification using targeted short read sequencingMarkus Riester	Markus Riester	software	28 Apr 2026	1,083	101
hgu95av2probe Probe sequence data for microarrays of type hgu95av2Bioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	1,064	42
puma Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)Xuejun Liu	Xuejun Liu	software	28 Apr 2026	1,033	55
scde Single Cell Differential ExpressionEvan Biederstedt	Evan Biederstedt	software	28 Apr 2026	1,033	50
affylmGUI GUI for limma Package with Affymetrix MicroarraysGordon Smyth	Gordon Smyth	software	28 Apr 2026	967	55
podkat Position-Dependent Kernel Association TestUlrich Bodenhofer	Ulrich Bodenhofer	software	28 Apr 2026	946	59
limmaGUI GUI for limma Package With Two Color MicroarraysGordon Smyth	Gordon Smyth	software	28 Apr 2026	905	11
hgu133aprobe Probe sequence data for microarrays of type hgu133aBioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	862	42
drosophila2probe Probe sequence data for microarrays of type drosophila2Bioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	861	42
hgu133acdf hgu133acdfBioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	858	42
mouse4302.db Affymetrix Affymetrix Mouse430_2 Array annotation data (chip mouse4302)Bioconductor Package Maintainer	Bioconductor Package Maintainer	annotation	no date on record	847	43
TRONCO TRONCO, an R package for TRanslational ONCOlogyLuca De Sano	Luca De Sano	software	28 Apr 2026	844	47
tigre Transcription factor Inference through Gaussian process Reconstruction of ExpressionAntti Honkela	Antti Honkela	software	28 Apr 2026	822	50
CoGAPS Coordinated Gene Activity in Pattern SetsElana J. Fertig	Elana J. Fertig	software	28 Apr 2026	805	94
wavClusteR Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP dataFederico Comoglio	Federico Comoglio	software	28 Apr 2026	791	148
bacon Controlling bias and inflation in association studies using the empirical null distributionMaarten van Iterson	Maarten van Iterson	software	28 Apr 2026	783	33