To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("GenomeInfoDb")

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

GenomeInfoDb

Utilities for manipulating chromosome and other 'seqname' identifiers

Bioconductor version: Release (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:

source("http://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 1.2.4
In Bioconductor since BioC 2.14 (R-3.1)
License Artistic-2.0
Depends R (>= 3.1), methods, stats4, BiocGenerics, S4Vectors(>= 0.2.0), IRanges(>= 1.99.26)
Imports methods, BiocGenerics, S4Vectors
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
System Requirements
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, 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

Package Archives

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

Package Source GenomeInfoDb_1.2.4.tar.gz
Windows Binary GenomeInfoDb_1.2.4.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) GenomeInfoDb_1.2.4.tgz
Mac OS X 10.9 (Mavericks) GenomeInfoDb_1.2.4.tgz
Browse/checkout source (username/password: readonly)
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