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Topic: Normalization or BSgenome or ChIPSeq

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Release: Release 3.12 (2020)

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323 packages on Bioconductor tagged Normalization or BSgenome or ChIPSeq, most distinct IPs first

Normalization, BSgenome and ChIPSeq 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
scuttle
Legacy Utilities for Single-Cell RNA-Seq AnalysisAaron Lun		Aaron Lunsoftware28 Apr 202614,23639
scater
Single-Cell Analysis Toolkit for Gene Expression Data in RAlan O'Callaghan		Alan O'Callaghansoftware2 Jul 202612,63578
sva
Surrogate Variable AnalysisJeffrey T. Leek		Jeffrey T. Leeksoftware5 May 202610,80468
scran
Methods for Single-Cell RNA-Seq Data AnalysisAaron Lun		Aaron Lunsoftware28 Apr 202610,13962
batchelor
Single-Cell Batch Correction MethodsAaron Lun		Aaron Lunsoftware28 Apr 20265,72056
BSgenome.Hsapiens.UCSC.hg38
Full genomic sequences for Homo sapiens (UCSC genome hg38)Bioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record4,98960
AUCell
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)Gert Hulselmans		Gert Hulselmanssoftware29 Apr 20264,610115
minfi
Analyze Illumina Infinium DNA methylation arraysKasper Daniel Hansen		Kasper Daniel Hansensoftware28 Apr 20264,041143
ChIPseeker
ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationGuangchuang Yu		Guangchuang Yusoftware28 Apr 20263,962158
variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experimentsGabriel E. Hoffman		Gabriel E. Hoffmansoftware28 Apr 20263,21199
ANCOMBC
Microbiome differential abudance and correlation analyses with bias correctionHuang Lin		Huang Linsoftware28 Apr 20263,000130
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
metagenomeSeq
Statistical analysis for sparse high-throughput sequencingJoseph N. Paulson		Joseph N. Paulsonsoftware28 Apr 20262,92432
BSgenome.Hsapiens.UCSC.hg19
Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13)Bioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record2,84258
Wrench
Wrench normalization for sparse count dataHector Corrada Bravo		Hector Corrada Bravosoftware28 Apr 20262,61911
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
BSgenome.Mmusculus.UCSC.mm10
Full genome sequences for Mus musculus (UCSC version mm10, based on GRCm38.p6)Bioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record2,15258
missMethyl
Analysing Illumina HumanMethylation BeadChip DataBelinda Phipson		Belinda Phipsonsoftware12 May 20261,987169
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
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
Maaslin2
"Multivariable Association Discovery in Population-scale Meta-omics Studies"Sagun Maharjan		Sagun Maharjansoftware28 Apr 20261,690133
ChAMP
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPICYuan Tian		Yuan Tiansoftware28 Apr 20261,643266