Rsubread: Subread sequence alignment for R

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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.

Author
Wei Shi and Yang Liao with contributions from Jenny Zhiyin Dai and Timothy Triche, Jr.
Date of publication
None
Maintainer
Wei Shi <shi@wehi.edu.au>
License
GPL-3
Version
1.24.0
URLs

View on Bioconductor

Man pages

align
Read mapping for genomic DNA-seq and RNA-seq data via...
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

Files in this package

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