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Topic: ChIPSeq or MicroarrayData or SystemsBiology

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Release: Release 3.7 (2018)

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262 packages on Bioconductor tagged ChIPSeq or MicroarrayData or SystemsBiology, most distinct IPs first

ChIPSeq, MicroarrayData and SystemsBiology 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
pathview
a tool set for pathway based data integration and visualizationWeijun Luo		Weijun Luosoftware28 Apr 20265,70650
ChIPseeker
ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationGuangchuang Yu		Guangchuang Yusoftware28 Apr 20263,962158
topGO
Enrichment Analysis for Gene OntologyFederico Marini		Federico Marinisoftware28 Apr 20263,22848
microbiome
Microbiome AnalyticsLeo Lahti		Leo Lahtisoftware28 Apr 20263,10980
regioneR
Association analysis of genomic regions based on permutation testsBernat Gel		Bernat Gelsoftware28 Apr 20262,95264
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,9518
ALDEx2
Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountGreg Gloor		Greg Gloorsoftware28 Apr 20262,53356
systemPipeR
systemPipeR: A Multipurpose Workflow Management System for Reproducible Data AnalysisThomas Girke		Thomas Girkesoftware28 Apr 20262,50694
DiffBind
Differential Binding Analysis of ChIP-Seq Peak DataRory Stark		Rory Starksoftware21 Jul 20262,490141
GENIE3
GEne Network Inference with Ensemble of treesVan Anh Huynh-Thu		Van Anh Huynh-Thusoftware28 Apr 20262,25326
viper
Virtual Inference of Protein-activity by Enriched Regulon analysisMariano J Alvarez		Mariano J Alvarezsoftware28 Apr 20262,06087
progeny
Pathway RespOnsive GENes for activity inference from gene expressionAurélien Dugourd		Aurélien Dugourdsoftware28 Apr 20262,01258
karyoploteR
Plot customizable linear genomes displaying arbitrary dataBernat Gel		Bernat Gelsoftware28 Apr 20261,962131
GreyListChIP
Grey Lists -- Mask Artefact Regions Based on ChIP InputsMatt Eldridge		Matt Eldridgesoftware28 Apr 20261,94259
gage
Generally Applicable Gene-set Enrichment for Pathway AnalysisWeijun Luo		Weijun Luosoftware28 Apr 20261,92944
ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval dataJianhong Ou		Jianhong Ousoftware10 Aug 20261,898125
motifStack
Plot stacked logos for single or multiple DNA, RNA and amino acid sequenceJianhong Ou		Jianhong Ousoftware28 Apr 20261,782111
chipseq
chipseq: A package for analyzing chipseq dataBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20261,62654
QuasR
Quantify and Annotate Short Reads in RMichael Stadler		Michael Stadlersoftware28 Apr 20261,551114
csaw
ChIP-Seq Analysis with WindowsAaron Lun		Aaron Lunsoftware28 Apr 20261,53646
derfinder
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approachLeonardo Collado-Torres		Leonardo Collado-Torressoftware28 Apr 20261,535137
IsoformSwitchAnalyzeR
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq dataKristoffer Vitting-Seerup		Kristoffer Vitting-Seerupsoftware28 Apr 20261,421151
hpar
Human Protein Atlas in RLaurent Gatto		Laurent Gattosoftware28 Apr 20261,38264
RedeR
Interactive visualization and manipulation of nested networksMauro Castro		Mauro Castrosoftware14 Jul 20261,31723
affydata
Affymetrix Data for Demonstration PurposeRobert D Shear		Robert D Shearexperiment5 May 20261,24412
ChIPQC
Quality metrics for ChIPseq dataTom Carroll		Tom Carrollsoftware19 May 20261,221159
INSPEcT
Modeling RNA synthesis, processing and degradation with RNA-seq dataStefano de Pretis		Stefano de Pretissoftware28 Apr 20261,213123