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Topic: SingleCell or Coverage

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Release: Release 3.4 (2016)

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76 packages on Bioconductor tagged SingleCell or Coverage, most distinct IPs first

SingleCell and Coverage in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
GenomicRanges
Representation and manipulation of genomic intervalsHervé Pagès		Hervé Pagèssoftware28 Apr 202656,97410
SummarizedExperiment
A container (S4 class) for matrix-like assaysHervé Pagès		Hervé Pagèssoftware28 Apr 202653,48424
edgeR
Empirical Analysis of Digital Gene Expression Data in RYunshun Chen		Yunshun Chensoftware19 Oct 202632,39210
Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file importBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202630,33728
GenomicAlignments
Representation and manipulation of short genomic alignmentsHervé Pagès		Hervé Pagèssoftware28 Apr 202627,00641
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
ensembldb
Utilities to create and use Ensembl-based annotation databasesJohannes Rainer		Johannes Rainersoftware25 May 202611,00080
scran
Methods for Single-Cell RNA-Seq Data AnalysisAaron Lun		Aaron Lunsoftware28 Apr 202610,13962
MAST
Model-based Analysis of Single Cell TranscriptomicsAndrew McDavid		Andrew McDavidsoftware28 Apr 20263,74056
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,9518
systemPipeR
systemPipeR: A Multipurpose Workflow Management System for Reproducible Data AnalysisThomas Girke		Thomas Girkesoftware28 Apr 20262,50694
bamsignals
Extract read count signals from bam filesJohannes Helmuth		Johannes Helmuthsoftware21 May 20262,20214
EnrichedHeatmap
Making Enriched HeatmapsZuguang Gu		Zuguang Gusoftware28 Apr 20262,00235
GreyListChIP
Grey Lists -- Mask Artefact Regions Based on ChIP InputsMatt Eldridge		Matt Eldridgesoftware28 Apr 20261,94259
DMRcate
Methylation array and sequencing spatial analysis methodsTim Peters		Tim Peterssoftware3 May 20261,838224
GenomicFiles
Distributed computing by file or by rangeBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20261,76380
rGREAT
GREAT Analysis - Functional Enrichment on Genomic RegionsZuguang Gu		Zuguang Gusoftware28 Apr 20261,663123
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
recount
Explore and download data from the recount projectLeonardo Collado-Torres		Leonardo Collado-Torressoftware28 Apr 20261,442162
SC3
Single-Cell Consensus ClusteringVladimir Kiselev		Vladimir Kiselevsoftware28 Apr 20261,36892
baySeq
Empirical Bayesian analysis of patterns of differential expression in count dataSamuel Granjeaud		Samuel Granjeaudsoftware28 Apr 20261,36420
PureCN
Copy number calling and SNV classification using targeted short read sequencingMarkus Riester		Markus Riestersoftware28 Apr 20261,356101
diffHic
Differential Analysis of Hi-C DataAaron Lun		Aaron Lunsoftware28 Apr 20261,15974
clusterExperiment
Compare Clusterings for Single-Cell SequencingElizabeth Purdom		Elizabeth Purdomsoftware28 Apr 20261,150147
traseR
GWAS trait-associated SNP enrichment analyses in genomic intervalsli chen		li chensoftware28 Apr 20261,14759
nucleR
Nucleosome positioning package for RAlba Sala		Alba Salasoftware28 Apr 20261,14576