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Topic: VariantAnnotation or Bayesian or ChipDb

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Release: Release 3.11 (2020)

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270 packages on Bioconductor tagged VariantAnnotation or Bayesian or ChipDb, most distinct IPs first

VariantAnnotation, Bayesian and ChipDb in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
limma
Linear Models for Microarray and Omics DataGordon Smyth		Gordon Smythsoftware10 Aug 202645,9656
edgeR
Empirical Analysis of Digital Gene Expression Data in RYunshun Chen		Yunshun Chensoftware19 Oct 202632,39210
DESeq2
Differential gene expression analysis based on the negative binomial distributionMichael Love		Michael Lovesoftware28 Apr 202632,07254
VariantAnnotation
Annotation of Genetic VariantsBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20269,66476
apeglm
Approximate posterior estimation for GLM coefficientsAnqi Zhu		Anqi Zhusoftware28 Apr 20267,71636
pcaMethods
A collection of PCA methodsHenning Redestig		Henning Redestigsoftware28 Apr 20267,38510
hgu133plus2.db
Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2)Bioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record4,22743
maftools
Summarize, Analyze and Visualize MAF FilesAnand Mayakonda		Anand Mayakondasoftware28 Apr 20263,52326
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,9518
infercnv
Infer Copy Number Variation from Single-Cell RNA-Seq DataChristophe Georgescu		Christophe Georgescusoftware28 Apr 20262,709194
ALDEx2
Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountGreg Gloor		Greg Gloorsoftware28 Apr 20262,53356
celda
CEllular Latent Dirichlet AllocationJoshua Campbell		Joshua Campbellsoftware28 Apr 20262,337127
hgu133a.db
Affymetrix Affymetrix HG-U133A Array annotation data (chip hgu133a)Bioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record1,99643
hgu95av2.db
Affymetrix Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2)Bioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record1,60543
baySeq
Empirical Bayesian analysis of patterns of differential expression in count dataSamuel Granjeaud		Samuel Granjeaudsoftware28 Apr 20261,36420
PureCN
Copy number calling and SNV classification using targeted short read sequencingMarkus Riester		Markus Riestersoftware28 Apr 20261,356101
hugene10sttranscriptcluster.db
Affymetrix hugene10 annotation data (chip hugene10sttranscriptcluster)Biocore Package Maintainer		Biocore Package Maintainerannotationno date on record1,30243
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 20261,29655
illuminaHumanv4.db
Illumina HumanHT12v4 annotation data (chip illuminaHumanv4)Mark Dunning		Mark Dunningannotationno date on record1,27443
BASiCS
Bayesian Analysis of Single-Cell Sequencing dataCatalina Vallejos		Catalina Vallejossoftware29 Apr 20261,206129
affylmGUI
GUI for limma Package with Affymetrix MicroarraysGordon Smyth		Gordon Smythsoftware28 Apr 20261,19455
scde
Single Cell Differential ExpressionEvan Biederstedt		Evan Biederstedtsoftware28 Apr 20261,17950
limmaGUI
GUI for limma Package With Two Color MicroarraysGordon Smyth		Gordon Smythsoftware28 Apr 20261,16511
podkat
Position-Dependent Kernel Association TestUlrich Bodenhofer		Ulrich Bodenhofersoftware28 Apr 20261,14359
normr
Normalization and difference calling in ChIP-seq dataJohannes Helmuth		Johannes Helmuthsoftware21 May 20261,06483
mouse4302.db
Affymetrix Affymetrix Mouse430_2 Array annotation data (chip mouse4302)Bioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record1,05843
DEqMS
a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.Yafeng Zhu		Yafeng Zhusoftware28 Apr 20261,05334
proDA
Differential Abundance Analysis of Label-Free Mass Spectrometry DataConstantin Ahlmann-Eltze		Constantin Ahlmann-Eltzesoftware28 Apr 20261,03428
TRONCO
TRONCO, an R package for TRanslational ONCOlogyLuca De Sano		Luca De Sanosoftware28 Apr 20261,02547
tigre
Transcription factor Inference through Gaussian process Reconstruction of ExpressionAntti Honkela		Antti Honkelasoftware28 Apr 20261,01350