Last data update: 2014.03.03
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coMET
Package: coMET
Type: Package
Title: coMET: visualisation of regional epigenome-wide association scan
(EWAS) results and DNA co-methylation patterns
Version: 1.4.4
Date: 2016-06-12
Author: Tiphaine C. Martin, Thomas Hardiman, Idil Yet, Pei-Chien Tsai, Jordana T. Bell
Maintainer: Tiphaine Martin <tiphaine.martin@kcl.ac.uk>
Description: Visualisation of EWAS results in a genomic region. In addition to phenotype-association P-values, coMET also generates plots of co-methylation patterns and provides a series of annotation tracks. It can be used to other omic-wide association scans as long as the data can be translated to genomic level and for any species.
Depends: R (>= 3.3.0), grid, utils, biomaRt, Gviz, psych
Suggests: knitr, RUnit, BiocGenerics, BiocStyle
Imports: colortools, hash, grDevices, gridExtra, rtracklayer, IRanges,
S4Vectors, GenomicRanges, ggbio, ggplot2, trackViewer, stats,
corrplot
License: GPL (>= 2)
URL: http://epigen.kcl.ac.uk/comet
biocViews: Software, DifferentialMethylation, Visualization,
Sequencing, Genetics, FunctionalGenomics, Microarray,
MethylationArray, MethylSeq, ChIPSeq, DNASeq, RiboSeq, RNASeq,
ExomeSeq, DNAMethylation, GenomeWideAssociation
VignetteBuilder: knitr
NeedsCompilation: no
Repository: Bioconductor
Packaged: 2016-06-13 05:03:36 UTC; biocbuild
● BiocViews: ChIPSeq, DNAMethylation, DNASeq, DifferentialMethylation, ExomeSeq, FunctionalGenomics, Genetics, GenomeWideAssociation, MethylSeq, MethylationArray, Microarray, RNASeq, RiboSeq, Sequencing, Software, Visualization
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18 images,
92 functions,
1 datasets
●
Reverse Depends: 0
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'coMET' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
** help
*** installing help indices
converting help for package 'coMET'
finding HTML links ... done
COSMIC_UCSC html
ChIPTF_ENCODE html
ClinVarCnv_UCSC html
ClinVarMain_UCSC html
CoreillCNV_UCSC html
DNAse_UCSC html
DNaseI_FANTOM html
DNaseI_RoadMap html
GAD_UCSC html
GWAScatalog_UCSC html
GeneReviews_UCSC html
HiCdata2matrix html
HistoneAll_UCSC html
HistoneOne_UCSC html
ISCA_UCSC html
TFBS_FANTOM html
bindingMotifsBiomart_ENSEMBL html
check.configVar html
check.configVar.cometlist html
check.format.mydata html
chrUCSC2ENSEMBL html
chromHMM_RoadMap html
chromatinHMMAll_UCSC html
chromatinHMMOne_UCSC html
coMET-package html
comet html
comet.list html
comet.web html
compute.cormatrix html
cpgIslands_UCSC html
cpgPvalue html
create.color.bar html
create.color.list html
create.color.list.large html
create.symbol.list html
create.symbol.list.large html
create.tracks.user html
create.tracks.web html
createList.trackUser html
datasets html
dgfootprints_RoadMap html
draw.legend html
draw.name.genes.web html
draw.name.tracks.web html
draw.plot.annotation html
draw.plot.axis.data html
draw.plot.comet html
draw.plot.comet.nopval html
draw.plot.comet.web html
draw.plot.cormatrix.plot html
draw.plot.grid.mydata html
draw.plot.grid.mydata.large html
draw.plot.grid.mydata.names html
draw.plot.grid.setup html
draw.plot.linesconnection html
draw.plot.mydata.ggbio html
eQTL html
eQTL_GTEx html
fix.values html
fix.values.generic html
fix.values.large html
gcContent_UCSC html
genesName_ENSEMBL html
genes_ENSEMBL html
imprintedGenes_GTEx html
interestGenes_ENSEMBL html
interestTranscript_ENSEMBL html
knownGenes_UCSC html
metQTL html
miRNATargetRegionsBiomart_ENSEMBL html
otherRegulatoryRegionsBiomart_ENSEMBL html
printPlot.comet html
printPlot.comet.nopval html
printPlot.comet.web html
psiQTL_GTEx html
read.config html
read.file.cormatrix html
read.file.mydata html
read.file.mydata.large html
refGenes_UCSC html
regulationBiomart_ENSEMBL html
regulatoryEvidenceBiomart_ENSEMBL html
regulatoryFeaturesBiomart_ENSEMBL html
regulatorySegmentsBiomart_ENSEMBL html
repeatMasker_UCSC html
retrieve.data html
segmentalDups_UCSC html
set.image.parameters html
snpBiomart_ENSEMBL html
snpLocations_UCSC html
structureBiomart_ENSEMBL html
transcript_ENSEMBL html
xenorefGenes_UCSC html
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
* DONE (coMET)
Making 'packages.html' ... done
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