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
Video
Simple tasks genomeInfoDb
Details
Version
1.6.3
In Bioconductor since
BioC 2.14 (R-3.1) (2 years)
License
Artistic-2.0
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
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
Package Archives
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