R-GenomicAlignments-1.4.1-1-rosa2014.1.i586.rpm


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Description

R-GenomicAlignments - Representation and manipulation of short genomic alignments

Property Value
Distribution ROSA 2014.1
Repository ROSA Contrib Updates i586
Package name R-GenomicAlignments
Package version 1.4.1
Package release 1-rosa2014.1
Package architecture i586
Package type rpm
Installed size 1.97 MB
Download size 1.27 MB
Official Mirror mirror.rosalab.ru
Provides efficient containers for storing and manipulating short genomic
alignments (typically obtained by aligning short reads to a reference
genome). This includes read counting, computing the coverage, junction
detection, and working with the nucleotide content of the alignments.

Alternatives

Package Version Architecture Repository
R-GenomicAlignments-1.4.1-1-rosa2014.1.x86_64.rpm 1.4.1 x86_64 ROSA Contrib Updates
R-GenomicAlignments - - -

Requires

Name Value
R-BSgenome -
R-BiocGenerics -
R-BiocParallel -
R-BiocStyle -
R-Biostrings -
R-DESeq -
R-GenomicFeatures -
R-GenomicRanges -
R-IRanges -
R-RUnit -
R-Rsamtools -
R-edgeR -
R-methods -
R-pasillaBamSubset -
R-rtracklayer -
R-stats -
libR.so -
libc.so.6 -
libc.so.6(GLIBC_2.0) -
libc.so.6(GLIBC_2.1.3) -
libc.so.6(GLIBC_2.3) -
libc.so.6(GLIBC_2.3.4) -
libc.so.6(GLIBC_2.4) -

Provides

Name Value
GenomicAlignments.so -
R-GenomicAlignments == 1.4.1-1:2014.1

Download

Type URL
Binary Package R-GenomicAlignments-1.4.1-1-rosa2014.1.i586.rpm
Source Package R-GenomicAlignments-1.4.1-1.src.rpm

Install Howto

  1. Enable ROSA Contrib Updates repository on Install and Remove Software
  2. Update packages list:
    # urpmi.update -a
  3. Install R-GenomicAlignments rpm package:
    # urpmi R-GenomicAlignments

Files

Path
/usr/lib/R/library/GenomicAlignments/CITATION
/usr/lib/R/library/GenomicAlignments/DESCRIPTION
/usr/lib/R/library/GenomicAlignments/INDEX
/usr/lib/R/library/GenomicAlignments/NAMESPACE
/usr/lib/R/library/GenomicAlignments/NEWS
/usr/lib/R/library/GenomicAlignments/Meta/Rd.rds
/usr/lib/R/library/GenomicAlignments/Meta/hsearch.rds
/usr/lib/R/library/GenomicAlignments/Meta/links.rds
/usr/lib/R/library/GenomicAlignments/Meta/nsInfo.rds
/usr/lib/R/library/GenomicAlignments/Meta/package.rds
/usr/lib/R/library/GenomicAlignments/Meta/vignette.rds
/usr/lib/R/library/GenomicAlignments/R/GenomicAlignments
/usr/lib/R/library/GenomicAlignments/R/GenomicAlignments.rdb
/usr/lib/R/library/GenomicAlignments/R/GenomicAlignments.rdx
/usr/lib/R/library/GenomicAlignments/doc/OverlapEncodings.R
/usr/lib/R/library/GenomicAlignments/doc/OverlapEncodings.Rnw
/usr/lib/R/library/GenomicAlignments/doc/OverlapEncodings.pdf
/usr/lib/R/library/GenomicAlignments/doc/WorkingWithAlignedNucleotides.R
/usr/lib/R/library/GenomicAlignments/doc/WorkingWithAlignedNucleotides.Rnw
/usr/lib/R/library/GenomicAlignments/doc/WorkingWithAlignedNucleotides.pdf
/usr/lib/R/library/GenomicAlignments/doc/index.html
/usr/lib/R/library/GenomicAlignments/doc/summarizeOverlaps.R
/usr/lib/R/library/GenomicAlignments/doc/summarizeOverlaps.Rnw
/usr/lib/R/library/GenomicAlignments/doc/summarizeOverlaps.pdf
/usr/lib/R/library/GenomicAlignments/extdata/sm_treated1.bam
/usr/lib/R/library/GenomicAlignments/extdata/sm_untreated1.bam
/usr/lib/R/library/GenomicAlignments/help/AnIndex
/usr/lib/R/library/GenomicAlignments/help/GenomicAlignments.rdb
/usr/lib/R/library/GenomicAlignments/help/GenomicAlignments.rdx
/usr/lib/R/library/GenomicAlignments/help/aliases.rds
/usr/lib/R/library/GenomicAlignments/help/paths.rds
/usr/lib/R/library/GenomicAlignments/html/00Index.html
/usr/lib/R/library/GenomicAlignments/html/GAlignmentPairs-class.html
/usr/lib/R/library/GenomicAlignments/html/GAlignments-class.html
/usr/lib/R/library/GenomicAlignments/html/GAlignmentsList-class.html
/usr/lib/R/library/GenomicAlignments/html/GappedReads-class.html
/usr/lib/R/library/GenomicAlignments/html/OverlapEncodings-class.html
/usr/lib/R/library/GenomicAlignments/html/R.css
/usr/lib/R/library/GenomicAlignments/html/cigar-utils.html
/usr/lib/R/library/GenomicAlignments/html/coordinate-mapping-methods.html
/usr/lib/R/library/GenomicAlignments/html/coverage-methods.html
/usr/lib/R/library/GenomicAlignments/html/encodeOverlaps-methods.html
/usr/lib/R/library/GenomicAlignments/html/findCompatibleOverlaps-methods.html
/usr/lib/R/library/GenomicAlignments/html/findMateAlignment.html
/usr/lib/R/library/GenomicAlignments/html/findOverlaps-methods.html
/usr/lib/R/library/GenomicAlignments/html/findSpliceOverlaps-methods.html
/usr/lib/R/library/GenomicAlignments/html/intra-range-methods.html
/usr/lib/R/library/GenomicAlignments/html/junctions-methods.html
/usr/lib/R/library/GenomicAlignments/html/mapCoords-methods.html
/usr/lib/R/library/GenomicAlignments/html/pileLettersAt.html
/usr/lib/R/library/GenomicAlignments/html/readGAlignments.html
/usr/lib/R/library/GenomicAlignments/html/sequenceLayer.html
/usr/lib/R/library/GenomicAlignments/html/setops-methods.html
/usr/lib/R/library/GenomicAlignments/html/stackStringsFromBam.html
/usr/lib/R/library/GenomicAlignments/html/summarizeOverlaps-methods.html
/usr/lib/R/library/GenomicAlignments/libs/GenomicAlignments.so
/usr/lib/R/library/GenomicAlignments/unitTests/test_GAlignments-class.R
/usr/lib/R/library/GenomicAlignments/unitTests/test_GAlignmentsList-class.R
/usr/lib/R/library/GenomicAlignments/unitTests/test_cigar-utils.R
/usr/lib/R/library/GenomicAlignments/unitTests/test_coordinate-mapping-methods.R
/usr/lib/R/library/GenomicAlignments/unitTests/test_findSpliceOverlaps-methods.R
/usr/lib/R/library/GenomicAlignments/unitTests/test_intra-range-methods.R
/usr/lib/R/library/GenomicAlignments/unitTests/test_readGAlignmentPairs.R
/usr/lib/R/library/GenomicAlignments/unitTests/test_readGAlignments.R
/usr/lib/R/library/GenomicAlignments/unitTests/test_readGAlignmentsList.R
/usr/lib/R/library/GenomicAlignments/unitTests/test_summarizeOverlaps-methods.R

Changelog

2015-07-10 - Denis Silakov <denis.silakov@rosalab.ru> 1.4.1-1
- (4fe402f) Build with BiocParallel

See Also

Package Description
R-GenomicFeatures-1.20.1-1-rosa2014.1.i586.rpm Tools for making and manipulating transcript centric annotations
R-GenomicRanges-1.20.5-1-rosa2014.1.i586.rpm Representation and manipulation of genomic intervals
R-HSAUR-1.3.6-1-rosa2014.1.i586.rpm A Handbook of Statistical Analyses Using R
R-Hmisc-3.16.0-1-rosa2014.1.i586.rpm Harrell Miscellaneous
R-IRanges-2.2.5-1-rosa2014.1.i586.rpm Infrastructure for manipulating intervals on sequences
R-LearnBayes-2.15-2-rosa2014.1.noarch.rpm Functions for Learning Bayesian Inference
R-MPV-1.38-2-rosa2014.1.noarch.rpm Data Sets from Montgomery, Peck and Vining's Book
R-MatchIt-2.4_21-3-rosa2014.1.noarch.rpm The skew-normal and skew-t distributions
R-OrganismDbi-1.10.0-1-rosa2014.1.i586.rpm Software to enable the smooth interfacing of different database packages
R-PBSmapping-2.69.76-1-rosa2014.1.i586.rpm Mapping Fisheries Data and Spatial Analysis Tools
R-R2HTML-2.3.1-3-rosa2014.1.i586.rpm HTML exportation for R objects
R-RANN-2.5-1-rosa2014.1.i586.rpm Fast Nearest Neighbour Search
R-RBGL-1.44.0-1-rosa2014.1.i586.rpm An interface to the BOOST graph library
R-RColorBrewer-1.1_2-1-rosa2014.1.noarch.rpm ColorBrewer palettes
R-RCurl-1.95.4.7-1-rosa2014.1.i586.rpm General network (HTTP/FTP/...) client interface for R
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