To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GenomeInfoDb")

In most cases, you don't need to download the package archive at all.

GenomeInfoDb

This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see GenomeInfoDb.

Utilities for manipulating chromosome and other 'seqname' identifiers

Bioconductor version: 3.0

Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.

Author: Sonali Arora, Martin Morgan, Marc Carlson, H. Pages

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

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GenomeInfoDb")

Documentation

To view documentation for the version of this package installed in your system, start R and enter: 

browseVignettes("GenomeInfoDb")
PDF R Script GenomeInfoDb :Introduction to GenomeInfoDb
PDF GenomeInfoDb: Submitting your organism to GenomeInfoDb
PDF Reference Manual
Text NEWS
Video Simple tasks genomeInfoDb

Details

biocViews Annotation, DataRepresentation, Genetics, GenomeAnnotation, Software
Version 1.2.5
In Bioconductor since BioC 2.14 (R-3.1) (2 years)
License Artistic-2.0
Depends R (>= 3.1), methods, stats4, BiocGenerics, S4Vectors(>= 0.2.0), IRanges(>= 1.99.26)
Imports methods, BiocGenerics, S4Vectors
LinkingTo
Suggests GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Dmelanogaster.UCSC.dm3.ensGene, RUnit, BiocStyle, knitr
SystemRequirements
Enhances
URL
Depends On Me AnnotationDbi, BSgenome, bumphunter, CSAR, GenomicAlignments, GenomicFeatures, GenomicRanges, GenomicTuples, gmapR, Gviz, htSeqTools, IdeoViz, methyAnalysis, Rsamtools, TitanCNA, VariantAnnotation
Imports Me AllelicImbalance, ballgown, biovizBase, BSgenome, casper, CexoR, ChIPseeker, CNEr, compEpiTools, csaw, derfinder, derfinderPlot, DNaseR, easyRNASeq, epivizr, exomeCopy, genoset, ggbio, GGtools, gwascat, h5vc, methylPipe, methylumi, MinimumDistance, NarrowPeaks, qpgraph, Rariant, regionReport, Repitools, rtracklayer, seqplots, SGSeq, ShortRead, SNPchip, SomaticSignatures, VanillaICE, VariantFiltering, VariantTools
Suggests Me QDNAseq
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source GenomeInfoDb_1.2.5.tar.gz
Windows Binary GenomeInfoDb_1.2.5.zip
Mac OS X 10.6 (Snow Leopard) GenomeInfoDb_1.2.5.tgz
Mac OS X 10.9 (Mavericks) GenomeInfoDb_1.2.5.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/GenomeInfoDb/tree/release-3.0
Package Short Url http://bioconductor.org/packages/GenomeInfoDb/
Package Downloads Report Download Stats

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