R-SRAdb-1.16.0-5-rosa2016.1.i586.rpm


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Description

R-SRAdb - A compilation of metadata from NCBI SRA and tools

Property Value
Distribution ROSA 2016.1
Repository ROSA Contrib i586
Package filename R-SRAdb-1.16.0-5-rosa2016.1.i586.rpm
Package name R-SRAdb
Package version 1.16.0
Package release 5-rosa2016.1
Package architecture i586
Package type rpm
Category Sciences/Mathematics
Homepage http://bioconductor.org/packages/release/bioc/html/SRAdb.html
License Artistic-2.0
Maintainer -
Download size 381.33 KB
Installed size 558.84 KB
The Sequence Read Archive (SRA) is the largest public repository of
sequencing data from the next generation of sequencing platforms including
Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD
System, Helicos Heliscope, and others. However, finding data of interest
can be challenging using current tools. SRAdb is an attempt to make access
to the metadata associated with submission, study, sample, experiment and
run much more feasible. This is accomplished by parsing all the NCBI SRA
metadata into a SQLite database that can be stored and queried locally.
Fulltext search in the package make querying metadata very flexible and
powerful.  fastq and sra files can be downloaded for doing alignment
locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp
protocol (ascp from Aspera Connect) for faster downloading large data
files over long distance. The SQLite database is updated regularly as new
data is added to SRA and can be downloaded at will for the most up-to-date

Alternatives

Package Version Architecture Repository
R-SRAdb-1.16.0-5-rosa2016.1.x86_64.rpm 1.16.0 x86_64 ROSA Contrib
R-SRAdb - - -

Requires

Name Value
R-GEOquery -
R-RCurl -
R-RSQLite -
R-graph -

Provides

Name Value
R-SRAdb == 1.16.0-5:2016.1

Download

Type URL
Mirror mirror.rosalab.ru
Binary Package R-SRAdb-1.16.0-5-rosa2016.1.i586.rpm
Source Package R-SRAdb-1.16.0-5.src.rpm

Install Howto

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

Files

Path
/usr/lib/R/library/SRAdb/CITATION
/usr/lib/R/library/SRAdb/DESCRIPTION
/usr/lib/R/library/SRAdb/INDEX
/usr/lib/R/library/SRAdb/NAMESPACE
/usr/lib/R/library/SRAdb/NEWS
/usr/lib/R/library/SRAdb/Meta/Rd.rds
/usr/lib/R/library/SRAdb/Meta/hsearch.rds
/usr/lib/R/library/SRAdb/Meta/links.rds
/usr/lib/R/library/SRAdb/Meta/nsInfo.rds
/usr/lib/R/library/SRAdb/Meta/package.rds
/usr/lib/R/library/SRAdb/R/SRAdb
/usr/lib/R/library/SRAdb/R/SRAdb.rdb
/usr/lib/R/library/SRAdb/R/SRAdb.rdx
/usr/lib/R/library/SRAdb/doc/SRAdb.R
/usr/lib/R/library/SRAdb/doc/SRAdb.Rnw
/usr/lib/R/library/SRAdb/doc/SRAdb.pdf
/usr/lib/R/library/SRAdb/extdata/SRR036007.chr1.hg18.bwa.sorted.bam
/usr/lib/R/library/SRAdb/extdata/SRR036007.chr1.hg18.bwa.sorted.bam.bai
/usr/lib/R/library/SRAdb/extdata/SRR036007.chr1.hg18.bwa.sorted.bam.tdf
/usr/lib/R/library/SRAdb/extdata/SRR036008.chr1.hg18.bwa.sorted.bam
/usr/lib/R/library/SRAdb/extdata/SRR036008.chr1.hg18.bwa.sorted.bam.bai
/usr/lib/R/library/SRAdb/extdata/SRR036008.chr1.hg18.bwa.sorted.bam.tdf
/usr/lib/R/library/SRAdb/help/AnIndex
/usr/lib/R/library/SRAdb/help/SRAdb.rdb
/usr/lib/R/library/SRAdb/help/SRAdb.rdx
/usr/lib/R/library/SRAdb/help/aliases.rds
/usr/lib/R/library/SRAdb/help/paths.rds
/usr/lib/R/library/SRAdb/html/00Index.html
/usr/lib/R/library/SRAdb/html/IGVclear.html
/usr/lib/R/library/SRAdb/html/IGVcollapse.html
/usr/lib/R/library/SRAdb/html/IGVgenome.html
/usr/lib/R/library/SRAdb/html/IGVgoto.html
/usr/lib/R/library/SRAdb/html/IGVload.html
/usr/lib/R/library/SRAdb/html/IGVsession.html
/usr/lib/R/library/SRAdb/html/IGVsnapshot.html
/usr/lib/R/library/SRAdb/html/IGVsocket.html
/usr/lib/R/library/SRAdb/html/IGVsort.html
/usr/lib/R/library/SRAdb/html/R.css
/usr/lib/R/library/SRAdb/html/SRAdb-package.html
/usr/lib/R/library/SRAdb/html/ascpR.html
/usr/lib/R/library/SRAdb/html/ascpSRA.html
/usr/lib/R/library/SRAdb/html/colDescriptions.html
/usr/lib/R/library/SRAdb/html/entityGraph.html
/usr/lib/R/library/SRAdb/html/getFASTQfile.html
/usr/lib/R/library/SRAdb/html/getFASTQinfo.html
/usr/lib/R/library/SRAdb/html/getSRA.html
/usr/lib/R/library/SRAdb/html/getSRAdbFile.html
/usr/lib/R/library/SRAdb/html/getSRAfile.html
/usr/lib/R/library/SRAdb/html/getSRAinfo.html
/usr/lib/R/library/SRAdb/html/listSRAfile.html
/usr/lib/R/library/SRAdb/html/sraConvert.html
/usr/lib/R/library/SRAdb/html/sraGraph.html
/usr/lib/R/library/SRAdb/html/startIGV.html

Changelog

2017-01-17 - Denis Silakov <dsilakov@virtuozzo.com> 1.16.0-5
- (6626a28) Revert bootstrap

See Also

Package Description
R-ShortRead-1.26.0-3-rosa2016.1.i586.rpm Classes and methods for high-throughput short-read sequencing data
R-Sleuth2-1.0.7-4-rosa2016.1.i586.rpm Data sets from Ramsey and Schafer's "Statistical Sleuth (2nd ed)"
R-Snowball-0.0.10-4-rosa2016.1.i586.rpm Snowball Stemmers
R-SnowballC-0.5.1-3-rosa2016.1.i586.rpm Snowball stemmers based on the C libstemmer UTF-8 library
R-SparseM-1.6-4-rosa2016.1.i586.rpm Sparse Linear Algebra
R-StanHeaders-2.14.0.1-1-rosa2016.1.i586.rpm C++ Header Files for Stan
R-TH.data-1.0.3-4-rosa2016.1.noarch.rpm TH's Data Archive
R-TSA-1.01-5-rosa2016.1.noarch.rpm Time Series Analysis
R-TSP-1.0.8-5-rosa2016.1.i586.rpm Traveling Salesperson Problem (TSP)
R-TeachingDemos-2.9-4-rosa2016.1.noarch.rpm Demonstrations for teaching and learning
R-TxDb.Hsapiens.UCSC.hg19.knownGene-2.10.1-4-rosa2016.1.noarch.rpm Annotation package for the Hsapiens_UCSC_hg19_knownGene_TxDb object
R-TxDb.Mmusculus.UCSC.mm9.knownGene-3.1.2-3-rosa2016.1.noarch.rpm Annotation package for TxDb object(s)
R-TxDb.Rnorvegicus.UCSC.rn5.refGene-2.10.1-4-rosa2016.1.noarch.rpm Annotation package for TranscriptDb object(s)
R-VGAM-0.9.8-3-rosa2016.1.i586.rpm Vector Generalized Linear and Additive Models
R-VGAMdata-0.9.7-3-rosa2016.1.noarch.rpm Data supporting the VGAM package
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