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Topic: SingleCell or SequencingData or Preprocessing

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Release: Release 3.2 (2015)

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204 packages on Bioconductor tagged SingleCell or SequencingData or Preprocessing, most distinct IPs first

SingleCell, SequencingData and Preprocessing 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
sva
Surrogate Variable AnalysisJeffrey T. Leek		Jeffrey T. Leeksoftware5 May 202610,80468
affy
Methods for Affymetrix Oligonucleotide ArraysRobert D. Shear		Robert D. Shearsoftware28 Apr 202610,55611
vsn
Variance stabilization and calibration for microarray dataWolfgang Huber		Wolfgang Hubersoftware28 Apr 20267,53633
biovizBase
Basic graphic utilities for visualization of genomic data.Michael Lawrence		Michael Lawrencesoftware28 Apr 20266,487126
oligo
Preprocessing tools for oligonucleotide arraysBenilton Carvalho		Benilton Carvalhosoftware28 Apr 20264,08752
minfi
Analyze Illumina Infinium DNA methylation arraysKasper Daniel Hansen		Kasper Daniel Hansensoftware28 Apr 20264,041143
HSMMSingleCell
Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)Cole Trapnell		Cole Trapnellexperiment5 May 20263,5530
marray
Exploratory analysis for two-color spotted microarray dataYee Hwa (Jean) Yang		Yee Hwa (Jean) Yangsoftware28 Apr 20263,3117
variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experimentsGabriel E. Hoffman		Gabriel E. Hoffmansoftware28 Apr 20263,21199
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,9518
airway
RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014Michael Love		Michael Loveexperiment5 May 20262,85425
methylumi
Handle Illumina methylation dataSean Davis		Sean Davissoftware16 Aug 20262,825158
flowWorkspace
Infrastructure for representing and interacting with gated and ungated cytometry data sets.Greg Finak		Greg Finaksoftware28 Apr 20262,80461
EDASeq
Exploratory Data Analysis and Normalization for RNA-SeqDavide Risso		Davide Rissosoftware28 Apr 20262,602111
aroma.light
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data TypesHenrik Bengtsson		Henrik Bengtssonsoftware28 Apr 20262,4818
lumi
BeadArray Specific Methods for Illumina Methylation and Expression MicroarraysLei Huang		Lei Huangsoftware28 Apr 20262,454165
affyPLM
Methods for fitting probe-level modelsBen Bolstad		Ben Bolstadsoftware28 Apr 20262,43022
Mfuzz
Soft clustering of omics time series dataMatthias Futschik		Matthias Futschiksoftware28 Apr 20262,35316
gcrma
Background Adjustment Using Sequence InformationZ. Wu		Z. Wusoftware28 Apr 20262,28521
openCyto
Hierarchical Gating Pipeline for flow cytometry dataMike Jiang		Mike Jiangsoftware28 Apr 20262,02875
GreyListChIP
Grey Lists -- Mask Artefact Regions Based on ChIP InputsMatt Eldridge		Matt Eldridgesoftware28 Apr 20261,94259
ballgown
Flexible, isoform-level differential expression analysisJack Fu		Jack Fusoftware4 Nov 20251,84487
DMRcate
Methylation array and sequencing spatial analysis methodsTim Peters		Tim Peterssoftware3 May 20261,838224
RUVSeq
Remove Unwanted Variation from RNA-Seq DataDavide Risso		Davide Rissosoftware28 Apr 20261,752116
beadarray
Quality assessment and low-level analysis for Illumina BeadArray dataMark Dunning		Mark Dunningsoftware31 Aug 20261,74065
wateRmelon
Illumina DNA methylation array normalization and metricsLeo C Schalkwyk		Leo C Schalkwyksoftware28 Apr 20261,720172
pasilla
Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011.Alejandro Reyes		Alejandro Reyesexperiment5 May 20261,554108
QuasR
Quantify and Annotate Short Reads in RMichael Stadler		Michael Stadlersoftware28 Apr 20261,551114