GenomicFeatures

Tools for making and manipulating transcript centric annotations

Bioconductor version: 2.8

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

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 Accessing Genome annotations from the UCSC Genome Browser
PDF R Script Making and Utilizing TranscriptDb Objects
PDF   Reference Manual

Details

biocViews Genetics, Infrastructure, Annotation, HighThroughputSequencing
Depends IRanges(>= 1.7.7), GenomicRanges(>= 1.3.23)
Imports methods, DBI (>= 0.2-5), RSQLite (>= 0.8-1), IRanges, GenomicRanges, Biostrings(>= 2.17.6), rtracklayer(>= 1.7.11), biomaRt, RCurl, utils
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 GenomicFeatures.Hsapiens.UCSC.hg18, GenomicFeatures.Mmusculus.UCSC.mm9
Imports Me geneLenDataBase, GenomicFeatures.Hsapiens.UCSC.hg18, GenomicFeatures.Mmusculus.UCSC.mm9
Suggests Me Biostrings, chipseq, GenomicRanges, ind1KG, Rsamtools
Version 1.4.5
Since Bioconductor 2.5 (R-2.10)

Package Downloads

Package Source GenomicFeatures_1.4.5.tar.gz
Windows Binary GenomicFeatures_1.4.5.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary GenomicFeatures_1.4.5.tgz
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