GenomeInfoDb

Utilities for manipulating chromosome and other 'seqname' identifiers

Bioconductor version: Release (2.14)

The Seqnames package 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>

To install this package, start R and enter:

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

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

Documentation

PDF R Script GenomeInfoDb :Introduction to GenomeInfoDb
PDF GenomeInfoDb: Submitting your organism to GenomeInfoDb
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, DataRepresentation, Genetics, Software
Version 1.0.2
In Bioconductor since BioC 2.14 (R-3.1)
License Artistic-2.0
Depends R (>= 3.1)
Imports
Suggests BiocGenerics, IRanges, BSgenome, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Dmelanogaster.UCSC.dm3.ensGene, RUnit, BiocStyle, knitr
System Requirements
URL
Depends On Me AnnotationDbi, GenomicRanges, Rsamtools
Imports Me GenomicFeatures, SomaticSignatures, VariantTools
Suggests Me BSgenome, QDNAseq

Package Downloads

Package Source GenomeInfoDb_1.0.2.tar.gz
Windows Binary GenomeInfoDb_1.0.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) GenomeInfoDb_1.0.2.tgz
Mac OS X 10.9 (Mavericks) GenomeInfoDb_1.0.2.tgz
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center