GenomicFeatures

Tools for making and manipulating transcript centric annotations

Bioconductor version: 2.9

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.

Author: M. Carlson, H. Pages, P. Aboyoun, S. Falcon, M. Morgan, D. Sarkar, M. Lawrence

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("GenomicFeatures")

To cite this package in a publication, start R and enter:

    citation("GenomicFeatures")

Documentation

PDF R Script Making and Utilizing TranscriptDb Objects
PDF   Reference Manual
Text   NEWS

Details

biocViews Genetics, Infrastructure, Annotation, HighThroughputSequencing
Depends IRanges(>= 1.11.34), GenomicRanges(>= 1.5.42), AnnotationDbi(>= 1.15.39)
Imports methods, DBI (>= 0.2-5), RSQLite (>= 0.8-1), IRanges, GenomicRanges, Biostrings(>= 2.17.6), rtracklayer(>= 1.13.14), biomaRt, RCurl, utils, Biobase
Suggests rtracklayer, biomaRt, org.Mm.eg.db, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg18(>= 1.3.14), BSgenome.Celegans.UCSC.ce2, RUnit
System Requirements
License Artistic-2.0
URL
Depends On Me ggtut, TxDb.Athaliana.BioMart.plantsmart10, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Scerevisiae.UCSC.sacCer2.ensGene, TxDb.Scerevisiae.UCSC.sacCer2.sgdGene
Imports Me geneLenDataBase, ggbio, TxDb.Athaliana.BioMart.plantsmart10, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Scerevisiae.UCSC.sacCer2.ensGene, TxDb.Scerevisiae.UCSC.sacCer2.sgdGene, VariantAnnotation
Suggests Me Biostrings, biovizBase, chipseq, GenomicRanges, ggtut, ind1KG, Rsamtools, ShortRead
Version 1.6.9
Since Bioconductor 2.5 (R-2.10)

Package Downloads

Package Source GenomicFeatures_1.6.9.tar.gz
Windows Binary GenomicFeatures_1.6.9.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary GenomicFeatures_1.6.9.tgz
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