Rsubread: Subread sequence alignment for R

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.
Date of publicationNone
MaintainerWei Shi <shi@wehi.edu.au>
LicenseGPL-3
Version1.24.1
http://bioconductor.org/packages/release/bioc/html/Rsubread.html

View on Bioconductor

Functions

align Man page
atgcContent Man page
buildindex Man page
createAnnotationFile Man page
detectionCall Man page
detectionCallAnnotation Man page
exactSNP Man page
featureCounts Man page
findCommonVariants Man page
getInBuiltAnnotation Man page
processExons Man page
propmapped Man page
qualityScores Man page
removeDupReads Man page
repair Man page
RsubreadUsersGuide Man page
sam2bed Man page
subjunc Man page
write.Rsubread Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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