Package: coMET 1.39.0

Tiphaine Martin

coMET: coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns

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 lon:g as the data can be translated to genomic level and for any species.

Authors:Tiphaine C. Martin [aut,cre], Thomas Hardiman [aut], Idil Yet [aut], Pei-Chien Tsai [aut], Jordana T. Bell [aut]

coMET_1.39.0.tar.gz
coMET_1.39.0.zip(r-4.5)coMET_1.39.0.zip(r-4.4)coMET_1.39.0.zip(r-4.3)
coMET_1.39.0.tgz(r-4.4-any)coMET_1.39.0.tgz(r-4.3-any)
coMET_1.39.0.tar.gz(r-4.5-noble)coMET_1.39.0.tar.gz(r-4.4-noble)
coMET_1.39.0.tgz(r-4.4-emscripten)coMET_1.39.0.tgz(r-4.3-emscripten)
coMET.pdf |coMET.html✨
coMET/json (API)
NEWS

# Install 'coMET' in R:
install.packages('coMET', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:coMET-1.39.0(bioc 3.21)coMET-1.38.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

softwaredifferentialmethylationvisualizationsequencinggeneticsfunctionalgenomicsmicroarraymethylationarraymethylseqchipseqdnaseqriboseqrnaseqexomeseqdnamethylationgenomewideassociationmotifannotation

5.18 score 15 scripts 200 downloads 18 mentions 54 exports 152 dependencies

Last updated 3 months agofrom:0dcb6aa416. Checks:1 OK, 6 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKDec 19 2024
R-4.5-winERRORDec 19 2024
R-4.5-linuxERRORDec 19 2024
R-4.4-winERRORDec 19 2024
R-4.4-macERRORDec 19 2024
R-4.3-winERRORDec 19 2024
R-4.3-macERRORDec 19 2024

Exports:bindingMotifsBiomart_ENSEMBLChIPTF_ENCODEchromatinHMMAll_UCSCchromatinHMMOne_UCSCchromHMM_RoadMapchrUCSC2ENSEMBLClinVarCnv_UCSCClinVarMain_UCSCcol2HSVcometcomet.listcomet.webcomplementaryCoreillCNV_UCSCCOSMIC_UCSCcpgIslands_UCSCdgfootprints_RoadMapDNaseI_FANTOMDNaseI_RoadMapeQTLeQTL_GTExGAD_UCSCgcContent_UCSCGeneReviews_UCSCgenes_ENSEMBLgenesName_ENSEMBLGWAScatalog_UCSCHiCdata2matrixHistoneAll_UCSCHistoneOne_UCSCimprintedGenes_GTExinterestGenes_ENSEMBLinterestTranscript_ENSEMBLknownGenes_UCSCmetQTLmiRNATargetRegionsBiomart_ENSEMBLoppositeotherRegulatoryRegionsBiomart_ENSEMBLpizzapsiQTL_GTExrefGenes_UCSCregulationBiomart_ENSEMBLregulatoryEvidenceBiomart_ENSEMBLregulatoryFeaturesBiomart_ENSEMBLregulatorySegmentsBiomart_ENSEMBLrepeatMasker_UCSCsegmentalDups_UCSCsetColorssnpBiomart_ENSEMBLsnpLocations_UCSCstructureBiomart_ENSEMBLTFBS_FANTOMtranscript_ENSEMBLxenorefGenes_UCSC

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecorrplotcpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2glueGPArotationgridExtragtableGvizhashhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemnormtmunsellnlmennetopensslpillarpkgconfigplogrpngprettyunitsprogressProtGenericspsychpurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc

coMET users guide

Rendered fromcoMET.Rnwusingknitr::knitron Dec 19 2024.

Last update: 2022-04-20
Started: 2014-12-13

Readme and manuals

Help Manual

Help pageTopics
visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns (and also for other omic-WAS)coMET-package coMET
Creates a binding motif track from ENSEMBLbindingMotifsBiomart_ENSEMBL
Creates a TF motif track from ENCODEChIPTF_ENCODE
Creating multiple chromHMM tracks from the UCSC genome browserchromatinHMMAll_UCSC
Creating one chromHMM track from the UCSC genome browserchromatinHMMOne_UCSC
Creates a ChromHMM track from a file of RoadMapchromHMM_RoadMap
Removing "chr" to the chromosome number from UCSC to transform it to ENSEMBL chromosome formatchrUCSC2ENSEMBL
Create one track of the genomic positions of variants from the ClinVar database (CNV only)ClinVarCnv_UCSC
Create one track of the genomic positions of variants from the ClinVar database (variants only)ClinVarMain_UCSC
col2HSV: converts a color to HSV in hexadecimal notationcol2HSV
Visualize EWAS results in a genomic region of interestcomet
List the correlations between omic featurescomet.list
Visualize EWAS results in a genomic region of interest with predefined annotation trackscomet.web
Complementary or opposite colorcomplementary opposite
Create one track of the genomic positions of CNV in chromosomal aberration and inherited disorders from the NIGMS Human Genetic Cell Repository dataCoreillCNV_UCSC
Create one track of the genomic positions of variants from COSMIC [obselete]COSMIC_UCSC
create track CpG Island from UCSCcpgIslands_UCSC
Creates a track of DNA motif positional bias in digital genomic Footprinting Sites (DGFP) from a file of RoadMapdgfootprints_RoadMap
Creation of an UCSC's DNase clusters track - obselete functionDNAse_UCSC
Creates a enhancer/promoter track from FANTOMDNaseI_FANTOM
Creates a promoter/enhancer regions track from a file of RoadMapDNaseI_RoadMap
Creates a track from a file for eQTL dataeQTL
Creates a eQTL track from GTExeQTL_GTEx
Create one track of the genomic positions of variants from the Genetic Association Database (GAD)GAD_UCSC
Create one track of GC content from UCSCgcContent_UCSC
Create one track of the genomic positions of variants from GeneReviewsGeneReviews_UCSC
Create one track of the genes in the genomic regions of interest from EMSEMBLgenes_ENSEMBL
Obtain the genes names in the genomic regions of interest from ENSEMBLgenesName_ENSEMBL
Create one track of the genomic positions of variants from the GWAS catalogGWAScatalog_UCSC
Creates a HiC matrix from a file (Rao et al., 2014)HiCdata2matrix
Create multiple tracks of histone modifications from the UCSC genome browserHistoneAll_UCSC
Create one track of one histone modification profile from the UCSC genome browserHistoneOne_UCSC
Creates a imprinted genes track from GTEximprintedGenes_GTEx
Create one track of the genes in the genomic regions of interest from EMSEMBLinterestGenes_ENSEMBL
Create a track of transcripts from ENSEMBLinterestTranscript_ENSEMBL
Create one track of the genomic positions of variants from ISCA [obselete database]ISCA_UCSC
Create a track of known genes from the UCSC genome browserknownGenes_UCSC
Creates a track from a file for metQTL datametQTL
Creates a track of miRNA target regions from ENSEMBLmiRNATargetRegionsBiomart_ENSEMBL
Creates a track of other regulatory regions from ENSEMBLotherRegulatoryRegionsBiomart_ENSEMBL
Pizza color wheelpizza
Creates a psiQTL track from GTExpsiQTL_GTEx
Create a track of RefSeq genes from the UCSC genome browserrefGenes_UCSC
Create a regulation track from ENSEMBLregulationBiomart_ENSEMBL
Creates a regulatory feature track from ENSEMBLregulatoryEvidenceBiomart_ENSEMBL
Creates a regulatory feature track from ENSEMBLregulatoryFeaturesBiomart_ENSEMBL
Creates a binding motif track from ENSEMBL [obselete]regulatorySegmentsBiomart_ENSEMBL
Create one track of the genomic positions of regions from repeatMasker_UCSCrepeatMasker_UCSC
Create one track of the genomic positions of regions from segmentalDups_UCSCsegmentalDups_UCSC
Set Colors for a color wheelsetColors
Create a short variation track from ENSEMBLsnpBiomart_ENSEMBL
Create a SNP track from UCSCsnpLocations_UCSC
Create a structural variation track from ENSEMBLstructureBiomart_ENSEMBL
Creates a TFBS motif track from FANTOMTFBS_FANTOM
Create a track of transcripts from ENSEMBLtranscript_ENSEMBL