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Topic: SingleCell or Coverage or GeneRegulation

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Release: Release 2.14 (2014)

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

SingleCell, Coverage and GeneRegulation in Topics

PackageMaintainerCategoryLatest versionDistinct IPs a monthNeeds
GenomicRanges
Representation and manipulation of genomic intervalsHervé Pagès		Hervé Pagèssoftware28 Apr 202656,97410
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
TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) AnalysisGe Tan		Ge Tansoftware28 Apr 20264,72179
Rsubread
Mapping, quantification and variant analysis of sequencing dataWei Shi		Wei Shisoftware28 Apr 20262,9518
CNEr
CNE Detection and VisualizationBoris Lenhard		Boris Lenhardsoftware28 Apr 20262,692112
DiffBind
Differential Binding Analysis of ChIP-Seq Peak DataRory Stark		Rory Starksoftware21 Jul 20262,490141
viper
Virtual Inference of Protein-activity by Enriched Regulon analysisMariano J Alvarez		Mariano J Alvarezsoftware28 Apr 20262,06087
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
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
qpgraph
Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics DataRobert Castelo		Robert Castelosoftware28 Apr 20261,49581
baySeq
Empirical Bayesian analysis of patterns of differential expression in count dataSamuel Granjeaud		Samuel Granjeaudsoftware28 Apr 20261,36420
nucleR
Nucleosome positioning package for RAlba Sala		Alba Salasoftware28 Apr 20261,14576
BCRANK
Predicting binding site consensus from ranked DNA sequencesAdam Ameur		Adam Ameursoftware28 Apr 20261,13815
rTRM
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction NetworksDiego Diez		Diego Diezsoftware28 Apr 20261,11747
MEDIPS
DNA IP-seq data analysisLukas Chavez		Lukas Chavezsoftware28 Apr 20261,093102
CexoR
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicatesPedro Madrigal		Pedro Madrigalsoftware28 Apr 20261,027101
RTN
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulonsMauro Castro		Mauro Castrosoftware28 Apr 20261,023142
triplex
Search and visualize intramolecular triplex-forming sequences in DNAJiri Hon		Jiri Honsoftware28 Apr 20261,02217
tigre
Transcription factor Inference through Gaussian process Reconstruction of ExpressionAntti Honkela		Antti Honkelasoftware28 Apr 20261,01350
CNVrd2
CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.Hoang Tan Nguyen		Hoang Tan Nguyensoftware28 Apr 20261,00191
tRanslatome
Comparison between multiple levels of gene expressionToma Tebaldi		Toma Tebaldisoftware28 Apr 2026956110
CRISPRseek
Design of guide RNAs in CRISPR genome-editing systemsLihua Julie Zhu		Lihua Julie Zhusoftware28 Apr 2026952141
GSRI
Gene Set Regulation IndexJulian Gehring		Julian Gehringsoftware28 Apr 202693664
Basic4Cseq
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq dataCarolin Walter		Carolin Waltersoftware29 Apr 202689661
rTRMui
A shiny user interface for rTRMDiego Diez		Diego Diezsoftware28 Apr 2026813101
CNAnorm
A normalization method for Copy Number Aberration in cancer samplesStefano Berri		Stefano Berrisoftware28 Apr 20268082