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Topic: Normalization or DimensionReduction or ChipDb

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Release: Release 3.3 (2016)

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231 packages on Bioconductor tagged Normalization or DimensionReduction or ChipDb, most distinct IPs first

Normalization, DimensionReduction 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
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
hgu133plus2.db
Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2)Bioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record4,22743
minfi
Analyze Illumina Infinium DNA methylation arraysKasper Daniel Hansen		Kasper Daniel Hansensoftware28 Apr 20264,041143
variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experimentsGabriel E. Hoffman		Gabriel E. Hoffmansoftware28 Apr 20263,21199
metagenomeSeq
Statistical analysis for sparse high-throughput sequencingJoseph N. Paulson		Joseph N. Paulsonsoftware28 Apr 20262,92432
DiffBind
Differential Binding Analysis of ChIP-Seq Peak DataRory Stark		Rory Starksoftware21 Jul 20262,490141
hgu133a.db
Affymetrix Affymetrix HG-U133A Array annotation data (chip hgu133a)Bioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record1,99643
missMethyl
Analysing Illumina HumanMethylation BeadChip DataBelinda Phipson		Belinda Phipsonsoftware12 May 20261,987169
ChAMP
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPICYuan Tian		Yuan Tiansoftware28 Apr 20261,643266
hgu95av2.db
Affymetrix Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2)Bioconductor Package Maintainer		Bioconductor Package Maintainerannotationno date on record1,60543
MSstats
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics ExperimentsMeena Choi		Meena Choisoftware28 Apr 20261,586100
csaw
ChIP-Seq Analysis with WindowsAaron Lun		Aaron Lunsoftware28 Apr 20261,53646
GENESIS
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatednessStephanie M. Gogarten		Stephanie M. Gogartensoftware28 Apr 20261,444117
Cardinal
A mass spectrometry imaging toolbox for statistical analysisKylie Ariel Bemis		Kylie Ariel Bemissoftware28 Apr 20261,40531
SC3
Single-Cell Consensus ClusteringVladimir Kiselev		Vladimir Kiselevsoftware28 Apr 20261,36892
hugene10sttranscriptcluster.db
Affymetrix hugene10 annotation data (chip hugene10sttranscriptcluster)Biocore Package Maintainer		Biocore Package Maintainerannotationno date on record1,30243
made4
Multivariate analysis of microarray data using ADE4Aedin Culhane		Aedin Culhanesoftware28 Apr 20261,27938
ACME
Algorithms for Calculating Microarray Enrichment (ACME)Sean Davis		Sean Davissoftware28 Apr 20261,2787
illuminaHumanv4.db
Illumina HumanHT12v4 annotation data (chip illuminaHumanv4)Mark Dunning		Mark Dunningannotationno date on record1,27443
quantro
A test for when to use quantile normalizationStephanie Hicks		Stephanie Hickssoftware28 Apr 20261,244153
affylmGUI
GUI for limma Package with Affymetrix MicroarraysGordon Smyth		Gordon Smythsoftware28 Apr 20261,19455
pcaExplorer
Interactive Visualization of RNA-seq Data Using a Principal Components ApproachFederico Marini		Federico Marinisoftware28 Apr 20261,192230
STATegRa
Classes and methods for multi-omics data integrationDavid Gomez-Cabrero		David Gomez-Cabrerosoftware28 Apr 20261,18746
limmaGUI
GUI for limma Package With Two Color MicroarraysGordon Smyth		Gordon Smythsoftware28 Apr 20261,16511
diffHic
Differential Analysis of Hi-C DataAaron Lun		Aaron Lunsoftware28 Apr 20261,15974