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Bioconductor - Rsubread (development version)

Rsubread

This is the development version of Rsubread; for the stable release version, see Rsubread.

Mapping, quantification and variant analysis of sequencing data

Bioconductor version: Development (3.22)

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.shi2 at monash.edu>, Yang Liao <yang.liao at monash.edu> and Gordon K Smyth <smyth at wehi.edu.au>

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("Rsubread")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Rsubread")
Details biocViews Alignment, ChIPSeq, GeneExpression, GeneFusionDetection, GeneRegulation, GeneticVariability, Genetics, GenomeAnnotation, ImmunoOncology, IndelDetection, MultipleSequenceAlignment, Preprocessing, QualityControl, RNASeq, SNP, SequenceMatching, Sequencing, SingleCell, Software, VariantAnnotation, VariantDetection Version 2.23.2 In Bioconductor since BioC 2.8 (R-2.13) (14 years) License GPL (>=3) Depends Imports grDevices, stats, utils, Matrix System Requirements URL http://bioconductor.org/packages/Rsubread See More Suggests Linking To Enhances Depends On Me ExCluster Imports Me APAlyzer, CleanUpRNAseq, Damsel, diffUTR, dupRadar, FRASER, ribosomeProfilingQC, scPipe, scruff, inDAGO Suggests Me autonomics, icetea, SpliceWiz, tidybulk, MetaScope Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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