Bioconductor – GenomeInfoDb

 
 

This package is for version 3.2 of Bioconductor;
for the stable, up-to-date release version, see
GenomeInfoDb.

Utilities for manipulating chromosome and other ‘seqname’ identifiers

Bioconductor version: 3.2

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

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 1.6.3
In Bioconductor since BioC 2.14 (R-3.1) (2 years)
License Artistic-2.0
Depends R (>= 3.1), methods, stats4, BiocGenerics(>= 0.13.8), S4Vectors(>= 0.7.11), 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 BSgenome, bsseq, bumphunter, ChIPComp, CODEX, CSAR, GenomicAlignments, GenomicFeatures, GenomicRanges, GenomicTuples, gmapR, groHMM, htSeqTools, IdeoViz, methyAnalysis, Rsamtools, SNPlocs.Hsapiens.dbSNP142.GRCh37, TitanCNA, VariantAnnotation, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38
Imports Me AllelicImbalance, AnnotationHubData, ballgown, biovizBase, BiSeq, BSgenome, casper, CexoR, ChIPpeakAnno, ChIPseeker, CNEr, CNPBayes, compEpiTools, conumee, CopywriteR, csaw, customProDB, derfinder, derfinderPlot, diffHic, easyRNASeq, ELMER, ensembldb, epivizr, exomeCopy, genomation, genomeIntervals, GenomicInteractions, genoset, genotypeeval, ggbio, GGtools, GoogleGenomics, gQTLstats, grasp2db, GreyListChIP, Gviz, gwascat, h5vc, HiTC, InPAS, IVAS, metagene, methylPipe, methylumi, minfi, MinimumDistance, motifbreakR, myvariant, NarrowPeaks, podkat, prebs, ProteomicsAnnotationHubData, qpgraph, QuasR, r3Cseq, RareVariantVis, Rariant, rCGH, regionReport, Repitools, RiboProfiling, rtracklayer, seqplots, SGSeq, ShortRead, SNPchip, SNPhood, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, soGGi, SomaticSignatures, SplicingGraphs, SummarizedExperiment, TarSeqQC, TFBSTools, VanillaICE, VariantFiltering, VariantTools, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38
Suggests Me AnnotationHub, gQTLBase, QDNAseq
Build Report  

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