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)
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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:

Datasets:

    On BioConductor:coMET-1.39.0(bioc 3.21)coMET-1.37.0(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 21 days agofrom:0dcb6aa416. Checks:OK: 1 ERROR: 6. Indexed: yes.

    TargetResultDate
    Doc / VignettesOKNov 19 2024
    R-4.5-winERRORNov 19 2024
    R-4.5-linuxERRORNov 19 2024
    R-4.4-winERRORNov 19 2024
    R-4.4-macERRORNov 19 2024
    R-4.3-winERRORNov 19 2024
    R-4.3-macERRORNov 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 Nov 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