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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicFeatures")
In most cases, you don't need to download the package archive at all.
GenomicFeatures
|
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 stat.math.ethz.ch>
Citation (from within R,
enter citation("GenomicFeatures")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicFeatures")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GenomicFeatures")
| examples.pdf | ||
| GenomicFeatures.pdf | ||
| Reference Manual |
Details
| 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 |
| LinkingTo | |
| Suggests | rtracklayer, biomaRt, org.Mm.eg.db, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg18(>= 1.3.14), BSgenome.Celegans.UCSC.ce2, RUnit |
| SystemRequirements | |
| Enhances | |
| 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 |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | GenomicFeatures_1.4.5.tar.gz |
| Windows Binary | GenomicFeatures_1.4.5.zip |
| Mac OS X 10.6 (Snow Leopard) | |
| Mac OS X 10.9 (Mavericks) | |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/GenomicFeatures/tree/release-2.8 |
| Package Short Url | http://bioconductor.org/packages/GenomicFeatures/ |
| Package Downloads Report | Download Stats |
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