Rsubread: Subread sequence alignment for R
Version 1.26.0

Provides powerful and easy-to-use tools for analyzing next-gen sequencing read data. Includes quality assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.

AuthorWei Shi and Yang Liao with contributions from Gordon Smyth, Jenny Dai and Timothy Triche, Jr.
Bioconductor views Alignment ChIPSeq GeneExpression GeneRegulation GeneticVariability Genetics GenomeAnnotation Preprocessing QualityControl RNASeq SNP SequenceMatching Sequencing Software
Date of publicationNone
MaintainerWei Shi <shi@wehi.edu.au>
LicenseGPL-3
Version1.26.0
URL http://bioconductor.org/packages/release/bioc/html/Rsubread.html
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Rsubread")

Popular man pages

align: Align sequence reads to a reference genome via seed-and-vote
buildindex: Build index for a reference genome
featureCounts: featureCounts: a general-purpose read summarization function
findCommonVariants: Finding the common variants among all input VCF files
getInBuiltAnnotation: Retrieve in-built annotations provided by featureCounts...
qualityScores: Extract quality score data in a sequencing read dataset
sam2bed: Convert a SAM format file to a BED format file
See all...

All man pages Function index File listing

Man pages

align: Align sequence reads to a reference genome via seed-and-vote
atgcContent: Calculate percentages of nucletodies A, T, G and C in a...
buildindex: Build index for a reference genome
createAnnotationFile: Create an annotation file from a GRanges object, suitable for...
detectionCall: Determine detection p values for each gene in an RNA-seq...
detectionCallAnnotation: Generate annotation data used for calculating detection p...
exactSNP: exactSNP - an accurate and efficient SNP caller
featureCounts: featureCounts: a general-purpose read summarization function
findCommonVariants: Finding the common variants among all input VCF files
getInBuiltAnnotation: Retrieve in-built annotations provided by featureCounts...
processExons: Obtain chromosomal coordiates of each exon using NCBI...
propmapped: Calculate the proportion of mapped reads/fragments in SAM/BAM...
qualityScores: Extract quality score data in a sequencing read dataset
removeDupReads: Remove sequencing reads which are mapped to identical...
repair: Re-order paired-end reads to place reads from the same pair...
RsubreadUsersGuide: View Rsubread Users Guide
sam2bed: Convert a SAM format file to a BED format file

Functions

Files

.BBSoptions
CHANGELOG
DESCRIPTION
NAMESPACE
NEWS
R
R/RsubreadUsersGuide.R
R/align.R
R/atgcContent.R
R/buildindex.R
R/createAnnotationFile.R
R/detectionCall.R
R/detectionCallAnnotation.R
R/exactSNP.R
R/featureCounts.R
R/findCommonVariants.R
R/getInBuiltAnnotation.R
R/processExons.R
R/propmapped.R
R/qualityScores.R
R/removeDupReads.R
R/repair.R
R/sam2bed.R
R/subjunc.R
build
build/vignette.rds
configure
inst
inst/CITATION
inst/annot
inst/annot/hg19_RefSeq_exon.txt
inst/annot/hg38_RefSeq_exon.txt
inst/annot/mm10_RefSeq_exon.txt
inst/annot/mm9_RefSeq_exon.txt
inst/doc
inst/doc/Rsubread.R
inst/doc/Rsubread.Rnw
inst/doc/Rsubread.pdf
inst/extdata
inst/extdata/reads.txt.gz
inst/extdata/reads1.txt.gz
inst/extdata/reads2.txt.gz
inst/extdata/reference.fa
inst/usersguide
inst/usersguide/SubreadUsersGuide.pdf
man
man/RsubreadUsersGuide.Rd
man/align.Rd
man/atgcContent.Rd
man/buildindex.Rd
man/createAnnotationFile.Rd
man/detectionCall.Rd
man/detectionCallAnnotation.Rd
man/exactSNP.Rd
man/featureCounts.Rd
man/findCommonVariants.Rd
man/getInBuiltAnnotation.Rd
man/processExons.Rd
man/propmapped.Rd
man/qualityScores.Rd
man/removeDupReads.Rd
man/repair.Rd
man/sam2bed.Rd
src
src/HelperFunctions.c
src/HelperFunctions.h
src/Makevars
src/Makevars.FreeBSD
src/Makevars.Linux
src/Makevars.MacOS
src/Makevars.SunOS
src/R_wrapper.c
src/SNPCalling.c
src/SNPCalling.h
src/aligner.c
src/atgcContent.c
src/build-sam-index.c
src/core-bigtable.c
src/core-bigtable.h
src/core-indel.c
src/core-indel.h
src/core-interface-aligner.c
src/core-interface-subjunc.c
src/core-junction.c
src/core-junction.h
src/core.c
src/core.h
src/detectionCall.c
src/detectionCallAnnotation.c
src/exon-algorithms.c
src/exon-algorithms.h
src/exon-align-indel.c
src/exon-align.c
src/fullscan.c
src/fusion-align.c
src/gene-algorithms.c
src/gene-algorithms.h
src/gene-value-index.c
src/gene-value-index.h
src/hashtable.c
src/hashtable.h
src/index-builder.c
src/input-files.c
src/input-files.h
src/interval_merge.c
src/interval_merge.h
src/long-hashtable.c
src/long-hashtable.h
src/mergeVCF.c
src/processExons.c
src/propmapped.c
src/qualityScores.c
src/read-repair.c
src/readSummary.c
src/removeDupReads.c
src/removeDupReads.h
src/sam2bed.c
src/sambam-file.c
src/sambam-file.h
src/seek-zlib.c
src/seek-zlib.h
src/sorted-hashtable.c
src/sorted-hashtable.h
src/sublog.c
src/sublog.h
src/subread.h
vignettes
vignettes/Rsubread.Rnw
Rsubread documentation built on May 20, 2017, 10:06 p.m.

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