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Topic: VariantAnnotation or Bayesian or ExpressionData

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Release: Release 2.12 (2013)

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22 packages on Bioconductor tagged VariantAnnotation or Bayesian or ExpressionData, most distinct IPs first

VariantAnnotation, Bayesian and ExpressionData 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
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,7228
baySeq
Empirical Bayesian analysis of patterns of differential expression in count dataSamuel Granjeaud		Samuel Granjeaudsoftware28 Apr 20261,16820
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
affylmGUI
GUI for limma Package with Affymetrix MicroarraysGordon Smyth		Gordon Smythsoftware28 Apr 202696755
limmaGUI
GUI for limma Package With Two Color MicroarraysGordon Smyth		Gordon Smythsoftware28 Apr 202690511
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
EBcoexpress
EBcoexpress for Differential Co-Expression AnalysisJohn A. Dawson		John A. Dawsonsoftware28 Apr 202672915
ternarynet
Ternary Network EstimationMcCall N. Matthew		McCall N. Matthewsoftware28 Apr 202658326
GRENITS
Gene Regulatory Network Inference Using Time SeriesEdward Morrissey		Edward Morrisseysoftware28 Apr 202653131
BitSeq
Transcript expression inference and differential expression analysis for RNA-seq data		no date on record426
ensemblVEP
R Interface to Ensembl Variant Effect Predictor		no date on record314
GeuvadisTranscriptExpr
Data package with transcript expression and bi-allelic genotypes from the GEUVADIS projectMalgorzata Nowicka		Malgorzata Nowickaexperiment5 May 20262950
networkBMA
Regression-based network inference using Bayesian Model Averaging		no date on record239
curatedBreastData
Curated breast cancer gene expression data with survival and treatment informationLevi Waldron		Levi Waldronexperiment23 Jul 202623177
mammaPrintData
RGLists from the Glas and Buyse breast cancer studiesLuigi Marchionni		Luigi Marchionniexperiment5 May 20262220
ccdata
Data for Combination Connectivity Mapping (ccmap) PackageAlex Pickering		Alex Pickeringexperiment5 May 20262000