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This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see 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>

Citation (from within R, enter citation("GenomicFeatures")):


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PDF examples.pdf
PDF GenomicFeatures.pdf
PDF   Reference Manual


biocViews Annotation, Genetics, HighThroughputSequencing, Infrastructure, Software
Version 1.4.5
In Bioconductor since BioC 2.5 (R-2.10) (6.5 years)
License Artistic-2.0
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,, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg18(>= 1.3.14), BSgenome.Celegans.UCSC.ce2, RUnit
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
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