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Topic: SingleCell or SequencingData or QualityControl

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Release: Release 3.4 (2016)

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220 packages on Bioconductor tagged SingleCell or SequencingData or QualityControl, most distinct IPs first

SingleCell, SequencingData and QualityControl 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
Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file importBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 202630,33728
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
ShortRead
FASTQ input and manipulationBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20268,12653
MSnbase
Base Functions and Classes for Mass Spectrometry and ProteomicsLaurent Gatto		Laurent Gattosoftware9 Aug 20265,521134
DECIPHER
Tools for curating, analyzing, and manipulating biological sequencesErik Wright		Erik Wrightsoftware30 Jul 20264,88216
monocle
Clustering, differential expression, and trajectory analysis for single- cell RNA-SeqCole Trapnell		Cole Trapnellsoftware28 Apr 20264,48574
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
variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experimentsGabriel E. Hoffman		Gabriel E. Hoffmansoftware28 Apr 20263,21199
interactiveDisplayBase
Base package for enabling powerful shiny web displays of Bioconductor objects		no date on record2,988
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
EDASeq
Exploratory Data Analysis and Normalization for RNA-SeqDavide Risso		Davide Rissosoftware28 Apr 20262,602111
systemPipeR
systemPipeR: A Multipurpose Workflow Management System for Reproducible Data AnalysisThomas Girke		Thomas Girkesoftware28 Apr 20262,50694
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
scRNAseq
Collection of Public Single-Cell RNA-Seq DatasetsAaron Lun		Aaron Lunexperiment5 May 20262,314121
DMRcate
Methylation array and sequencing spatial analysis methodsTim Peters		Tim Peterssoftware3 May 20261,838224
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
pRoloc
A unifying bioinformatics framework for spatial proteomicsLisa Breckels		Lisa Breckelssoftware28 Apr 20261,689230
GWASTools
Tools for Genome Wide Association StudiesStephanie M. Gogarten		Stephanie M. Gogartensoftware28 Apr 20261,63494
chipseq
chipseq: A package for analyzing chipseq dataBioconductor Package Maintainer		Bioconductor Package Maintainersoftware28 Apr 20261,62654
MSstats
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics ExperimentsMeena Choi		Meena Choisoftware28 Apr 20261,586100