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Topic: SingleCell or SequencingData or DNAMethylation

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Release: Release 3.6 (2017)

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189 packages on Bioconductor tagged SingleCell or SequencingData or DNAMethylation, most distinct IPs first

SingleCell, SequencingData and DNAMethylation in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
edgeR
Empirical Analysis of Digital Gene Expression Data in RYunshun Chen		Yunshun Chensoftware19 Oct 202632,39210
SingleCellExperiment
S4 Classes for Single Cell DataDavide Risso		Davide Rissosoftware28 Apr 202624,48325
HDF5Array
HDF5 datasets as array-like objects in RHervé Pagès		Hervé Pagèssoftware28 Apr 202620,53728
scater
Single-Cell Analysis Toolkit for Gene Expression Data in RAlan O'Callaghan		Alan O'Callaghansoftware2 Jul 202612,63578
scran
Methods for Single-Cell RNA-Seq Data AnalysisAaron Lun		Aaron Lunsoftware28 Apr 202610,13962
TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC dataTiago Chedraoui Silva		Tiago Chedraoui Silvasoftware28 Apr 20266,750103
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
bumphunter
Bump HunterTamilselvi Guharaj		Tamilselvi Guharajsoftware28 Apr 20264,26883
minfi
Analyze Illumina Infinium DNA methylation arraysKasper Daniel Hansen		Kasper Daniel Hansensoftware28 Apr 20264,041143
MAST
Model-based Analysis of Single Cell TranscriptomicsAndrew McDavid		Andrew McDavidsoftware28 Apr 20263,74056
HSMMSingleCell
Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)Cole Trapnell		Cole Trapnellexperiment5 May 20263,5530
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
bsseq
Analyze, manage and store whole-genome methylation dataKasper Daniel Hansen		Kasper Daniel Hansensoftware28 Apr 20262,71889
lumi
BeadArray Specific Methods for Illumina Methylation and Expression MicroarraysLei Huang		Lei Huangsoftware28 Apr 20262,454165
scRNAseq
Collection of Public Single-Cell RNA-Seq DatasetsAaron Lun		Aaron Lunexperiment5 May 20262,314121
chromVAR
Chromatin Variation Across RegionsAlicia Schep		Alicia Schepsoftware11 May 20262,255134
missMethyl
Analysing Illumina HumanMethylation BeadChip DataBelinda Phipson		Belinda Phipsonsoftware12 May 20261,987169
DMRcate
Methylation array and sequencing spatial analysis methodsTim Peters		Tim Peterssoftware3 May 20261,838224
methylKit
DNA methylation analysis from high-throughput bisulfite sequencing resultsAltuna Akalin		Altuna Akalinsoftware28 Apr 20261,83399
EpiDISH
Epigenetic Dissection of Intra-Sample-HeterogeneityShijie C. Zheng		Shijie C. Zhengsoftware28 Apr 20261,79363
IlluminaHumanMethylation450kmanifest
Annotation for Illumina's 450k methylation arraysKasper Daniel Hansen		Kasper Daniel Hansenannotationno date on record1,773144
wateRmelon
Illumina DNA methylation array normalization and metricsLeo C Schalkwyk		Leo C Schalkwyksoftware28 Apr 20261,720172
DSS
Dispersion shrinkage for sequencing dataHao Wu		Hao Wusoftware28 Apr 20261,70291
ChAMP
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPICYuan Tian		Yuan Tiansoftware28 Apr 20261,643266
multiMiR
Integration of multiple microRNA-target databases with their disease and drug associationsSpencer Mahaffey		Spencer Mahaffeysoftware28 Apr 20261,56953
zinbwave
Zero-Inflated Negative Binomial Model for RNA-Seq DataDavide Risso		Davide Rissosoftware28 Apr 20261,56974
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
splatter
Simple Simulation of Single-cell RNA Sequencing DataLuke Zappia		Luke Zappiasoftware28 Apr 20261,55361