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Topic: VariantAnnotation or Bayesian or MicroarrayData

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Release: Release 3.4 (2016)

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158 packages on Bioconductor tagged VariantAnnotation or Bayesian or MicroarrayData, most distinct IPs first

VariantAnnotation, Bayesian and MicroarrayData in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
limma
Linear Models for Microarray and Omics DataGordon Smyth		Gordon Smythsoftware10 Aug 202644,6566
DESeq2
Differential gene expression analysis based on the negative binomial distributionMichael Love		Michael Lovesoftware28 Apr 202631,84554
edgeR
Empirical Analysis of Digital Gene Expression Data in RYunshun Chen		Yunshun Chensoftware19 Oct 202631,06510
VariantAnnotation
Annotation of Genetic VariantsBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20269,77176
pcaMethods
A collection of PCA methodsHenning Redestig		Henning Redestigsoftware28 Apr 20267,21410
maftools
Summarize, Analyze and Visualize MAF FilesAnand Mayakonda		Anand Mayakondasoftware28 Apr 20263,41926
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,7228
ALDEx2
Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountGreg Gloor		Greg Gloorsoftware28 Apr 20262,31156
baySeq
Empirical Bayesian analysis of patterns of differential expression in count dataSamuel Granjeaud		Samuel Granjeaudsoftware28 Apr 20261,16820
affydata
Affymetrix Data for Demonstration PurposeRobert D Shear		Robert D Shearexperiment5 May 20261,16112
PureCN
Copy number calling and SNV classification using targeted short read sequencingMarkus Riester		Markus Riestersoftware28 Apr 20261,083101
puma
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)Xuejun Liu		Xuejun Liusoftware28 Apr 20261,03355
scde
Single Cell Differential ExpressionEvan Biederstedt		Evan Biederstedtsoftware28 Apr 20261,03350
affylmGUI
GUI for limma Package with Affymetrix MicroarraysGordon Smyth		Gordon Smythsoftware28 Apr 202696755
bladderbatch
Bladder gene expression data illustrating batch effectsJeffrey T. Leek		Jeffrey T. Leekexperiment5 May 20269497
podkat
Position-Dependent Kernel Association TestUlrich Bodenhofer		Ulrich Bodenhofersoftware28 Apr 202694659
limmaGUI
GUI for limma Package With Two Color MicroarraysGordon Smyth		Gordon Smythsoftware28 Apr 202690511
normr
Normalization and difference calling in ChIP-seq dataJohannes Helmuth		Johannes Helmuthsoftware21 May 202686683
TRONCO
TRONCO, an R package for TRanslational ONCOlogyLuca De Sano		Luca De Sanosoftware28 Apr 202684447
tigre
Transcription factor Inference through Gaussian process Reconstruction of ExpressionAntti Honkela		Antti Honkelasoftware28 Apr 202682250
CoGAPS
Coordinated Gene Activity in Pattern SetsElana J. Fertig		Elana J. Fertigsoftware28 Apr 202680594
wavClusteR
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP dataFederico Comoglio		Federico Comogliosoftware28 Apr 2026791148
HelloRanges
Introduce *Ranges to bedtools usersMichael Lawrence		Michael Lawrencesoftware28 Apr 202678378
bacon
Controlling bias and inflation in association studies using the empirical null distributionMaarten van Iterson		Maarten van Itersonsoftware28 Apr 202678333
ASSIGN
Adaptive Signature Selection and InteGratioN (ASSIGN)Ying Shen		Ying Shensoftware28 Apr 202677093
TVTB
TVTB: The VCF Tool BoxKevin Rue-Albrecht		Kevin Rue-Albrechtsoftware28 Apr 2026758159
minfiData
Example data for the Illumina Methylation 450k arrayKasper Daniel Hansen		Kasper Daniel Hansenexperiment5 May 2026731146
EBcoexpress
EBcoexpress for Differential Co-Expression AnalysisJohn A. Dawson		John A. Dawsonsoftware28 Apr 202672915
PCAN
Phenotype Consensus ANalysis (PCAN)Matthew Page		Matthew Pagesoftware28 Apr 202672914
R3CPET
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet ProcessMohamed Nadhir Djekidel		Mohamed Nadhir Djekidelsoftware28 Apr 2026727139