DOI: 10.18129/B9.bioc.Rsubread  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see Rsubread.

Mapping, quantification and variant analysis of sequencing data

Bioconductor version: 3.16

Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads.

Author: Wei Shi, Yang Liao and Gordon K Smyth with contributions from Jenny Dai

Maintainer: Wei Shi <wei.shi at>, Yang Liao <yang.liao at> and Gordon K Smyth <smyth at>

Citation (from within R, enter citation("Rsubread")):


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PDF R Script Rsubread Vignette
PDF SubreadUsersGuide.pdf
PDF   Reference Manual
Text   NEWS


biocViews Alignment, ChIPSeq, GeneExpression, GeneFusionDetection, GeneRegulation, GeneticVariability, Genetics, GenomeAnnotation, ImmunoOncology, IndelDetection, MultipleSequenceAlignment, Preprocessing, QualityControl, RNASeq, SNP, SequenceMatching, Sequencing, SingleCell, Software, VariantAnnotation, VariantDetection
Version 2.12.3
In Bioconductor since BioC 2.8 (R-2.13) (12 years)
License GPL (>=3)
Imports grDevices, stats, utils, Matrix
Depends On Me ExCluster
Imports Me APAlyzer, diffUTR, dupRadar, FRASER, ribosomeProfilingQC, scPipe, scruff
Suggests Me autonomics, icetea, NxtIRFcore, singleCellTK, SpliceWiz, tidybulk
Links To Me
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