Rsamtools
This package is for version 3.1 of Bioconductor;
for the stable, up-to-date release version, see
Rsamtools.
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Bioconductor version: 3.1
This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.
Author: Martin Morgan, Herv\'e Pag\`es, Valerie Obenchain, Nathaniel Hayden
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
Citation (from within R,
enter citation("Rsamtools")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Rsamtools")
Documentation
To view documentation for the version of this package installed
in your system, start R and enter:
browseVignettes("Rsamtools")
Video
pileup in Rsamtools
Details
Version
1.20.5
In Bioconductor since
BioC 2.6 (R-2.11) (6 years)
License
Artistic-2.0 | file LICENSE
Suggests
GenomicAlignments,
ShortRead(>= 1.19.10),
GenomicFeatures,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
KEGG.db,
TxDb.Hsapiens.UCSC.hg18.knownGene,
RNAseqData.HNRNPC.bam.chr14,
BSgenome.Hsapiens.UCSC.hg19,
pasillaBamSubset,
RUnit,
BiocStyle
SystemRequirements
Enhances
Depends On Me
ArrayExpressHTS,
BitSeq,
chimera,
CODEX,
CoverageView,
exomeCopy,
exomePeak,
GenomicAlignments,
GenomicFiles,
ggtut,
girafe,
leeBamViews,
MEDIPS,
methylPipe,
MMDiff,
oneChannelGUI,
podkat,
qrqc,
r3Cseq,
Rcade,
ReQON,
rfPred,
RIPSeeker,
rnaSeqMap,
ShortRead,
ssviz,
systemPipeR,
TBX20BamSubset,
TEQC,
TitanCNA,
VariantAnnotation,
wavClusteR
Imports Me
AllelicImbalance,
annmap,
ArrayExpressHTS,
biovizBase,
BSgenome,
CAGEr,
casper,
CexoR,
ChIPQC,
cn.mops,
CNVrd2,
compEpiTools,
CopywriteR,
csaw,
customProDB,
derfinder,
DEXSeq,
diffHic,
DOQTL,
easyRNASeq,
EDASeq,
epigenomix,
FourCSeq,
FunciSNP,
genomation,
GenomicAlignments,
GenomicInteractions,
ggbio,
GGtools,
gmapR,
GoogleGenomics,
GreyListChIP,
Gviz,
gwascat,
h5vc,
HTSeqGenie,
LungCancerLines,
MafDb.ALL.wgs.phase1.release.v3.20101123,
MafDb.ALL.wgs.phase3.release.v5a.20130502,
MafDb.ESP6500SI.V2.SSA137,
MafDb.ExAC.r0.3.sites,
metagene,
nucleR,
PICS,
QDNAseq,
QuasR,
R453Plus1Toolbox,
Rariant,
Repitools,
RNAprobR,
rtracklayer,
SGSeq,
similaRpeak,
soGGi,
SplicingGraphs,
tracktables,
trackViewer,
TransView,
VariantFiltering,
VariantTools
Suggests Me
AnnotationHub,
bamsignals,
BaseSpaceR,
BiocParallel,
biomvRCNS,
DiffBind,
gage,
GenomeInfoDb,
GenomicFeatures,
GenomicRanges,
gQTLstats,
ind1KG,
metaseqR,
parathyroidSE,
RnaSeqTutorial,
seqbias,
SigFuge,
Streamer
Package Archives
Follow
Installation instructions to use this
package in your R session.