GenomicFeatures

Tools for making and manipulating transcript centric annotations

Bioconductor version: 2.10

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	R Script	Representing Transcripts as Splice Graphs
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Genetics, HighThroughputSequencing, Infrastructure, Software
Depends	BiocGenerics(>= 0.1.0), IRanges(>= 1.13.10), GenomicRanges(>= 1.7.17), AnnotationDbi(>= 1.15.39)
Imports	methods, DBI (>= 0.2-5), RSQLite (>= 0.8-1), BiocGenerics, IRanges, GenomicRanges, Biostrings(>= 2.23.2), rtracklayer(>= 1.15.1), biomaRt, RCurl, utils, Biobase(>= 2.15.1)
Suggests	rtracklayer, biomaRt, org.Mm.eg.db, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg18(>= 1.3.14), BSgenome.Celegans.UCSC.ce2, mirbase.db, FDb.UCSC.tRNAs, RUnit, TxDb.Hsapiens.UCSC.hg18.knownGene
System Requirements
License	Artistic-2.0
URL
Depends On Me	FDb.UCSC.tRNAs, ggtut, TxDb.Athaliana.BioMart.plantsmart10, TxDb.Athaliana.BioMart.plantsmart12, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Mmusculus.UCSC.mm10.ensGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Scerevisiae.UCSC.sacCer2.sgdGene
Imports Me	biovizBase, FDb.UCSC.tRNAs, geneLenDataBase, ggbio, TxDb.Athaliana.BioMart.plantsmart10, TxDb.Athaliana.BioMart.plantsmart12, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Mmusculus.UCSC.mm10.ensGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Scerevisiae.UCSC.sacCer2.sgdGene, VariantAnnotation
Suggests Me	Biostrings, chipseq, easyRNASeq, GenomicRanges, ggtut, ind1KG, Rsamtools, ShortRead
Version	1.8.3
Since	Bioconductor 2.5 (R-2.10)

Package Downloads

Package Source	GenomicFeatures_1.8.3.tar.gz
Windows Binary	GenomicFeatures_1.8.3.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	GenomicFeatures_1.8.3.tgz
Package Downloads Report	Download Stats