R-GenomicFeatures-1.14.2-2.fc21.noarch.rpm


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Description

R-GenomicFeatures - Tools for making and manipulating transcript centric annotations

Distribution: Fedora Rawhide
Repository: Fedora x86_64
Package name: R-GenomicFeatures
Package version: 1.14.2
Package release: 2.fc21
Package architecture: noarch
Package type: rpm
Installed size: 2.51 MB
Download size: 974.12 KB
Official Mirror: dl.fedoraproject.org
A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.

Alternatives

Provides

  • R-GenomicFeatures = 1.14.2-2.fc21

    Install Howto

    Install the R-GenomicFeatures rpm package:

    # dnf install R-GenomicFeatures

    Files

    • /usr/share/R/library/GenomicFeatures/DESCRIPTION
    • /usr/share/R/library/GenomicFeatures/INDEX
    • /usr/share/R/library/GenomicFeatures/NAMESPACE
    • /usr/share/R/library/GenomicFeatures/NEWS
    • /usr/share/R/library/GenomicFeatures/Meta/Rd.rds
    • /usr/share/R/library/GenomicFeatures/Meta/hsearch.rds
    • /usr/share/R/library/GenomicFeatures/Meta/links.rds
    • /usr/share/R/library/GenomicFeatures/Meta/nsInfo.rds
    • /usr/share/R/library/GenomicFeatures/Meta/package.rds
    • /usr/share/R/library/GenomicFeatures/R/GenomicFeatures
    • /usr/share/R/library/GenomicFeatures/R/GenomicFeatures.rdb
    • /usr/share/R/library/GenomicFeatures/R/GenomicFeatures.rdx
    • /usr/share/R/library/GenomicFeatures/doc/GenomicFeatures.R
    • /usr/share/R/library/GenomicFeatures/doc/GenomicFeatures.Rnw
    • /usr/share/R/library/GenomicFeatures/doc/GenomicFeatures.pdf
    • /usr/share/R/library/GenomicFeatures/extdata/Aedes_aegypti.partial.gtf
    • /usr/share/R/library/GenomicFeatures/extdata/Biomart_Ensembl_sample.sqlite
    • /usr/share/R/library/GenomicFeatures/extdata/FeatureDb.sqlite
    • /usr/share/R/library/GenomicFeatures/extdata/NC_011025.gff.txt
    • /usr/share/R/library/GenomicFeatures/extdata/TESTFLYGFF3.sqlite
    • /usr/share/R/library/GenomicFeatures/extdata/TESTGFF.sqlite
    • /usr/share/R/library/GenomicFeatures/extdata/TESTGTF.sqlite
    • /usr/share/R/library/GenomicFeatures/extdata/UCSC_knownGene_sample.rda
    • /usr/share/R/library/GenomicFeatures/extdata/UCSC_knownGene_sample.sqlite
    • /usr/share/R/library/GenomicFeatures/extdata/UCSC_knownToLocusLink_sample.rda
    • /usr/share/R/library/GenomicFeatures/extdata/a.gff3
    • /usr/share/R/library/GenomicFeatures/extdata/cD.exByEdge-SG-Vig.Rda
    • /usr/share/R/library/GenomicFeatures/extdata/cD.exsByGenes-SG-Vig.Rda
    • /usr/share/R/library/GenomicFeatures/extdata/dmel-1000-r5.11.filtered.gff
    • /usr/share/R/library/GenomicFeatures/extdata/events.Rda
    • /usr/share/R/library/GenomicFeatures/help/AnIndex
    • /usr/share/R/library/GenomicFeatures/help/GenomicFeatures.rdb
    • /usr/share/R/library/GenomicFeatures/help/GenomicFeatures.rdx
    • /usr/share/R/library/GenomicFeatures/help/aliases.rds
    • /usr/share/R/library/GenomicFeatures/help/paths.rds
    • /usr/share/R/library/GenomicFeatures/html/00Index.html
    • /usr/share/R/library/GenomicFeatures/html/DEFAULT_CIRC_SEQS.html
    • /usr/share/R/library/GenomicFeatures/html/FeatureDb-class.html
    • /usr/share/R/library/GenomicFeatures/html/R.css
    • /usr/share/R/library/GenomicFeatures/html/TranscriptDb-class.html
    • /usr/share/R/library/GenomicFeatures/html/as-format-methods.html
    • /usr/share/R/library/GenomicFeatures/html/deprecated.html
    • /usr/share/R/library/GenomicFeatures/html/extractTranscriptsFromGenome.html
    • /usr/share/R/library/GenomicFeatures/html/features.html
    • /usr/share/R/library/GenomicFeatures/html/getPromoterSeq-methods.html
    • /usr/share/R/library/GenomicFeatures/html/id2name.html
    • /usr/share/R/library/GenomicFeatures/html/makeFeatureDbFromUCSC.html
    • /usr/share/R/library/GenomicFeatures/html/makeTranscriptDb.html
    • /usr/share/R/library/GenomicFeatures/html/makeTranscriptDbFromBiomart.html
    • /usr/share/R/library/GenomicFeatures/html/makeTranscriptDbFromGFF.html
    • /usr/share/R/library/GenomicFeatures/html/makeTranscriptDbFromUCSC.html
    • /usr/share/R/library/GenomicFeatures/html/makeTxDbPackage.html
    • /usr/share/R/library/GenomicFeatures/html/nearest-methods.html
    • /usr/share/R/library/GenomicFeatures/html/regions.html
    • /usr/share/R/library/GenomicFeatures/html/saveFeatures.html
    • /usr/share/R/library/GenomicFeatures/html/select-methods.html
    • /usr/share/R/library/GenomicFeatures/html/transcripts.html
    • /usr/share/R/library/GenomicFeatures/html/transcriptsBy.html
    • /usr/share/R/library/GenomicFeatures/html/transcriptsByOverlaps.html
    • /usr/share/R/library/GenomicFeatures/script/makeTxDbs.R
    • /usr/share/R/library/GenomicFeatures/script/maketRNAFDb.R
    • /usr/share/R/library/GenomicFeatures/txdb-template/DESCRIPTION
    • /usr/share/R/library/GenomicFeatures/txdb-template/NAMESPACE
    • /usr/share/R/library/GenomicFeatures/txdb-template/R/zzz.R
    • /usr/share/R/library/GenomicFeatures/txdb-template/inst/
    • /usr/share/R/library/GenomicFeatures/txdb-template/inst/extdata/
    • /usr/share/R/library/GenomicFeatures/txdb-template/man/package.Rd
    • /usr/share/R/library/GenomicFeatures/unitTests/test_TranscriptDb_seqinfo.R
    • /usr/share/R/library/GenomicFeatures/unitTests/test_getPromoterSeq-methods.R
    • /usr/share/R/library/GenomicFeatures/unitTests/test_makeIdsForUniqueDataFrameRows.R
    • /usr/share/R/library/GenomicFeatures/unitTests/test_makeTranscriptDb.R
    • /usr/share/R/library/GenomicFeatures/unitTests/test_makeTranscriptDbFromBiomart.R
    • /usr/share/R/library/GenomicFeatures/unitTests/test_makeTranscriptDbFromGFF.R
    • /usr/share/R/library/GenomicFeatures/unitTests/test_makeTranscriptDbFromUCSC.R
    • /usr/share/R/library/GenomicFeatures/unitTests/test_select-methods.R
    • /usr/share/R/library/GenomicFeatures/unitTests/test_transcripts.R
    • /usr/share/R/library/GenomicFeatures/unitTests/test_transcriptsBy.R
    • /usr/share/R/library/GenomicFeatures/unitTests/test_transcriptsByOverlaps.R

    Changelog

    2014-06-06 - Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.14.2-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild

    2014-01-27 - pingou <pingou@pingoured.fr> 1.14.2-1 - Update to version 1.14.2

    2013-08-02 - Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.12.2-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild

    2013-07-16 - pingou <pingou@pingoured.fr> 1.12.2-1 - Update to version 1.12.2

    2013-04-07 - pingou <pingou@pingoured.fr> 1.12.0-1 - Update to version 1.12.0

    2013-02-28 - pingou <pingou@pingoured.fr> 1.10.2-1 - Update to version 1.10.2

    2013-02-13 - Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.10.1-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild

    2012-11-27 - pingou <pingou@pingoured.fr> 1.10.1-1 - Update to version 1.10.1

    2012-07-18 - Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.6.1-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild

    2012-01-12 - Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.6.1-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild

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