Rsamtools-package: 'samtools' aligned sequence utilities interface

Description Details Note Author(s) References Examples

Description

This package provides facilities for parsing samtools BAM (binary) files representing aligned sequences.

Details

See packageDescription('Rsamtools') for package details. A useful starting point is the scanBam manual page.

Note

This package documents the following classes for purely internal reasons, see help pages in other packages: bzfile, fifo, gzfile, pipe, unz, url.

Author(s)

Author: Martin Morgan

Maintainer: Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>

References

The current source code for samtools and bcftools is from https://github.com/samtools/samtools. Additional material is at http://samtools.sourceforge.net/.

Examples

1
packageDescription('Rsamtools')

Example output

Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
sh: 1: wc: Permission denied
sh: 1: cannot create /dev/null: Permission denied
'BiocParallel' did not register default BiocParallelParams:
  missing value where TRUE/FALSE needed
Package: Rsamtools
Type: Package
Title: Binary alignment (BAM), FASTA, variant call (BCF), and tabix
        file import
Version: 1.26.2
Author: Martin Morgan, Herv\'e Pag\`es, Valerie Obenchain, Nathaniel
        Hayden
Maintainer: Bioconductor Package Maintainer
        <maintainer@bioconductor.org>
Description: 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.
URL: http://bioconductor.org/packages/release/bioc/html/Rsamtools.html
License: Artistic-2.0 | file LICENSE
LazyLoad: yes
Depends: methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.21.6),
        Biostrings (>= 2.37.1)
Imports: utils, BiocGenerics (>= 0.1.3), S4Vectors (>= 0.7.11), IRanges
        (>= 2.3.7), XVector (>= 0.9.1), zlibbioc, bitops, BiocParallel
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
LinkingTo: S4Vectors, IRanges, XVector, Biostrings
biocViews: DataImport, Sequencing, Coverage, Alignment, QualityControl
Video:
        https://www.youtube.com/watch?v=Rfon-DQYbWA&list=UUqaMSQd_h-2EDGsU6WDiX0Q
NeedsCompilation: yes
Packaged: 2017-04-07 22:38:00 UTC; biocbuild
Built: R 3.4.0; x86_64-pc-linux-gnu; "Wed, 10 May 2017 05:15:03 +0000";
        unix

-- File: /usr/lib/R/site-library/Rsamtools/Meta/package.rds 

Rsamtools documentation built on May 31, 2017, 2:56 p.m.

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