Files in TiphaineCMartin/coMET_original
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/AnalyseFile.R R/BiofeatureGraphics.R R/DrawPlot.R R/GeneralMethodComet.R R/comet.R R/cometWeb.R R/cometlist.R README.md
data/BindingMotifAll.rda
data/BindingMotifMultiple.rda
data/BindingMotifSingle.rda
data/ClinVarCnvTrack.rda
data/CoreillCNVTrack.rda
data/DNaseI_RoadMapSingle.rda
data/DupTrack.rda
data/GWASTrack.rda
data/GeneReviewTrack.rda
data/GeneReviewsTrack.rda
data/ISCAtrack.rda
data/ISCAtrack_Grch38.rda
data/OtherRegulatoryRegionsAll.rda
data/OtherRegulatoryRegionsSingle.rda
data/PancreasIG.rda
data/PancreasIGtrack.rda
data/PancreasimprintedIG.rda
data/PancreasimprintedIGtrack.rda
data/RegulatoryEvidenceBiomartAll.rda
data/RegulatoryEvidenceBiomartMultiple.rda
data/RegulatoryEvidenceBiomartSingle.rda
data/RegulatoryFeaturesBiomartAll.rda
data/RegulatoryFeaturesBiomartMultiple.rda
data/RegulatoryFeaturesBiomartSingle.rda
data/RegulatorySegmentsBiomartAll.rda
data/RegulatorySegmentsBiomartMultiple.rda
data/RegulatorySegmentsBiomartSingle.rda
data/SegmentalDupsUCSC.rda
data/StomachIG.rda
data/StomachIGtrack.rda
data/allIG.rda
data/allIGtrack.rda
data/allimprintedIG.rda
data/allimprintedIGtrack.rda
data/bindMotifsBiomartTrackAll.rda
data/bindMotifsBiomartTrackMultiple.rda
data/bindMotifsBiomartTrackSingle.rda
data/bindingMotifsBiomartAll.rda
data/bindingMotifsBiomartMultiple.rda
data/bindingMotifsBiomartSingle.rda
data/chipTFtrack.rda
data/chipTFtrack_old.rda
data/chromHMM_RoadMapAll.rda
data/chromHMM_RoadMapAllE063.rda
data/chromHMM_RoadMapMultiple.rda
data/chromHMM_RoadMapSingle.rda
data/chromatinHMMRoadMapAll.rda
data/chromatinHMMRoadMapMultiple.rda
data/chromatinHMMRoadMapSingle.rda
data/chromhmmNoPattern.rda
data/chromhmmPattern.rda
data/chromhmmtrackone.rda
data/clinVarMaintrack.rda
data/coreilVarianttrack.rda
data/cosmicVarianttrack.rda
data/cpgIslandsUCSC.rda
data/cpgIslandtrack.rda
data/dgfootprints_RoadMapSingle.rda
data/dnasetrack.rda
data/dyaRM.rda
data/dyaRMtrack.rda
data/eGTexTrackSNP.rda
data/eGTexTrackall.rda
data/eQTLAll.rda
data/eQTLMultiple.rda
data/eQTLSingle.rda
data/eQTLTrackAll.rda
data/eQTLTrackMultiple.rda
data/eQTLTrackSingle.rda
data/enhFANTOMtrack.rda
data/enhRM.rda
data/enhRMtrack.rda
data/gadtrack.rda
data/gcContent.rda
data/gctrack.rda
data/geneENSEMBLtrack.rda
data/geneNameEnsembl.rda
data/genesENSEMBL.rda
data/genesGencodetrack.rda
data/genesNameENSEMBL.rda
data/genesUcsctrack.rda
data/genetrack4RM.rda
data/genetrack4psiGTEX.rda
data/grtrack4eGTex.rda
data/histonalltrack.rda
data/histoneonetrack.rda
data/imprintedGenesGTEx.rda
data/interestGenesENSEMBL.rda
data/interestTranscriptENSEMBL.rda
data/interestgenesENSMBLtrack.rda
data/interesttransENSMBLtrack.rda
data/knownGenesUCSC.rda
data/matrix_HiC_Rao.rda
data/metQTLSingle.rda
data/metQTLTrackAll.rda
data/metQTLTrackMultiple.rda
data/metQTLTrackSingle.rda
data/miRNATargetRegionsBiomart.rda
data/miRNATargetRegionsBiomartTrack.rda
data/otherRegulatoryRegionsTrackAll.rda
data/otherRegulatoryRegionsTrackSingle.rda
data/promRMtrack.rda
data/promRMtrackE063.rda
data/psiGTex.rda
data/psiGTexTrackSNP.rda
data/psiGTexTrackall.rda
data/refGenesUCSC.rda
data/regulationENSEMBLtrack.rda
data/regulatoryEvidenceBiomartTrackAll.rda
data/regulatoryEvidenceBiomartTrackMultiple.rda
data/regulatoryEvidenceBiomartTrackSingle.rda
data/regulatoryFeaturesBiomartTrackAll.rda
data/regulatoryFeaturesBiomartTrackMultiple.rda
data/regulatoryFeaturesBiomartTrackSingle.rda
data/regulatorySegmentsBiomartTrackAll.rda
data/regulatorySegmentsBiomartTrackMultiple.rda
data/regulatorySegmentsBiomartTrackSingle.rda
data/repeatMaskerTrack.rda
data/snpBiomart.rda
data/snpBiomarttrack.rda
data/snpUCSCtrack.rda
data/snptrack.rda
data/strucBiomarttrack.rda
data/structureBiomart.rda
data/tfbsFANTOMtrack.rda
data/transENSMBLtrack.rda
data/xenogenestrack.rda
data/xenorefGenesUCSC.rda
inst/CITATION
inst/doc/coMET.pdf
inst/extdata/RoadMap.bed
inst/extdata/config_cyp1b1_zoom.txt
inst/extdata/config_cyp1b1_zoom_4comet.txt
inst/extdata/config_cyp1b1_zoom_4cometnopval.txt
inst/extdata/config_cyp1b1_zoom_4cometnopval_Grch38.txt
inst/extdata/config_cyp1b1_zoom_4nomatrix.txt
inst/extdata/config_cyp1b1_zoom_4nomatrix_Grch38.txt
inst/extdata/config_cyp1b1_zoom_4webserver.txt
inst/extdata/config_cyp1b1_zoom_4webserver.txt~
inst/extdata/config_cyp1b1_zoom_4webserver_Grch38.txt
inst/extdata/config_gata55_larger_article.txt
inst/extdata/config_gata55_larger_article_rev.txt
inst/extdata/cyp1b1_infofile.bed
inst/extdata/cyp1b1_infofile.txt
inst/extdata/cyp1b1_infofile_Grch38.txt
inst/extdata/cyp1b1_infofile_bed.txt
inst/extdata/cyp1b1_infofile_bed_v2.bed
inst/extdata/cyp1b1_infofile_bed_v2.txt
inst/extdata/cyp1b1_infofile_bed_v2_hg38.bed
inst/extdata/cyp1b1_infofile_bed_v3.bed
inst/extdata/cyp1b1_infofile_bed_v3.txt
inst/extdata/cyp1b1_infofile_bed_v3_hg38.bed
inst/extdata/cyp1b1_infofile_exprGene_region.txt
inst/extdata/cyp1b1_infofile_exprGene_region_Grch38.txt
inst/extdata/cyp1b1_infofile_exprGene_region_v2.csv
inst/extdata/cyp1b1_res37_cormatrix_list_BH05.txt
inst/extdata/cyp1b1_res37_rawMatrix.txt
inst/extdata/cyp1b1_zoom_plus_name_expr.pdf
inst/extdata/datalist
inst/extdata/eQTL.bed
inst/extdata/gata4_55probes_info.txt
inst/extdata/gata4_55probes_rawMatrix.txt
inst/extdata/gata4_55probes_residuals.txt
inst/extdata/gata4_95probes_info.txt
inst/extdata/gata_comet_55probes_large_article.eps
inst/extdata/gata_comet_55probes_large_article_gene.eps
inst/extdata/gata_comet_55probes_large_article_rev.eps
inst/extdata/metQTL.bed
inst/unitTests/ChangeLog.txt
inst/unitTests/Citation.txt
inst/unitTests/test_chrUCSC2ENSEMBL.R man/COSMICTrack.Rd man/COSMIC_UCSC.Rd man/ChIPTF_ENCODE.Rd man/ClinVarCnvTrack.Rd man/ClinVarCnv_UCSC.Rd man/ClinVarMain_UCSC.Rd man/CoreillCNVTrack.Rd man/CoreillCNV_UCSC.Rd man/DNAse_UCSC.Rd man/DNaseI_FANTOM.Rd man/DNaseI_RoadMap.Rd man/GAD_UCSC.Rd man/GWAScatalog_UCSC.Rd man/GeneReviews_UCSC.Rd man/HiCdata2matrix.Rd man/HistoneAll_UCSC.Rd man/HistoneOne_UCSC.Rd man/ISCA_UCSC.Rd man/OtherRegulatoryRegionsBiomart.Rd man/RegulatoryFeaturesBiomart .Rd man/RegulatorySegmentsBiomart.Rd man/SegmentalDupsUCSC.Rd man/TFBS_FANTOM.Rd man/bindingMotifsBiomart_ENSEMBL.Rd man/check.configVar.Rd man/check.configVar.cometlist.Rd man/check.format.mydata.Rd man/chrUCSC2ENSEMBL.Rd man/chromHMM_RoadMap.Rd man/chromatinHMMAll.Rd man/chromatinHMMAll_UCSC.Rd man/chromatinHMMOne_UCSC.Rd man/chromatinHMMRoadMap.Rd man/coMET-package.Rd man/comet.Rd man/comet.list.Rd man/comet.web.Rd man/compute.cormatrix.Rd man/cpgIslands_UCSC.Rd man/cpgPvalue.Rd man/create.color.bar.Rd man/create.color.list.Rd man/create.color.list.large.Rd man/create.symbol.list.Rd man/create.symbol.list.large.Rd man/create.tracks.user.Rd man/create.tracks.web.Rd man/createList.trackUser.Rd man/datasets.Rd man/dgfootprints_RoadMap.Rd man/draw.legend.Rd man/draw.name.genes.web.Rd man/draw.name.tracks.web.Rd man/draw.plot.annotation.Rd man/draw.plot.axis.data.Rd man/draw.plot.comet.Rd man/draw.plot.comet.nopval.Rd man/draw.plot.comet.web.Rd man/draw.plot.cormatrix.plot.Rd man/draw.plot.grid.mydata.Rd man/draw.plot.grid.mydata.large.Rd man/draw.plot.grid.mydata.names.Rd man/draw.plot.grid.setup.Rd man/draw.plot.linesconnection.Rd man/draw.plot.mydata.ggbio.Rd man/eQTL.Rd man/eQTL_GTEx.Rd man/fix.values.Rd man/fix.values.generic.Rd man/fix.values.large.Rd man/gcContent_UCSC.Rd man/genesName_ENSEMBL.Rd man/genes_ENSEMBL.Rd man/imprintedGenes_GTEx.Rd man/interestGenes_ENSEMBL.Rd man/interestTranscript_ENSEMBL.Rd man/knownGenesUCSC.Rd man/knownGenes_UCSC.Rd man/metQTL.Rd man/miRNATargetRegionsBiomart.Rd man/miRNATargetRegionsBiomart_ENSEMBL.Rd man/otherRegulatoryRegionsBiomart_ENSEMBL.Rd man/printPlot.comet.Rd man/printPlot.comet.nopval.Rd man/printPlot.comet.web.Rd man/psiQTL_GTEx.Rd man/read.config.Rd man/read.file.cormatrix.Rd man/read.file.mydata.Rd man/read.file.mydata.large.Rd man/refGenes_UCSC.Rd man/regulationBiomart_ENSEMBL.Rd man/regulatoryEvidenceBiomart_ENSEMBL.Rd man/regulatoryFeaturesBiomart_ENSEMBL.Rd man/regulatorySegmentsBiomart_ENSEMBL.Rd man/repeatMasker_UCSC.Rd man/retrieve.data.Rd man/segmentalDups_UCSC.Rd man/set.image.parameters.Rd man/snpBiomart_ENSEMBL.Rd man/snpLocations_UCSC.Rd man/structureBiomart_ENSEMBL.Rd man/transcript_ENSEMBL.Rd man/xenorefGenes_UCSC.Rd tests/runTests.R
vignettes/biblio.bib
vignettes/coMET-package.R vignettes/coMET.R
vignettes/coMET.Rnw
vignettes/figure/minimal-FANTOM_example2-1.pdf vignettes/figure/minimal-GTEX_example12-1.pdf vignettes/figure/minimal-GTEX_example4e2-1.pdf vignettes/figure/minimal-GTEX_example5e2-1.pdf vignettes/figure/minimal-GenesAndTranscript2-1.pdf vignettes/figure/minimal-Roadmap_example1e2-1.pdf vignettes/figure/minimal-cometPlot-1.pdf vignettes/figure/minimal-cometPlotMatrix-1.pdf vignettes/figure/minimal-cometPlot_matrix-1.pdf vignettes/figure/minimal-cometPlot_nomatrix-1.pdf vignettes/figure/minimal-cometPlot_nopval-1.pdf vignettes/figure/minimal-cometPlotfile-1.pdf vignettes/figure/minimal-cometwebPlot-1.pdf vignettes/figure/minimal-encode_example2-1.pdf vignettes/figure/minimal-encore_genes2-1.pdf vignettes/figure/minimal-extract_data_1kb2-1.pdf
www/DESCRIPTION
www/Readme.md
www/config_cyp1b1_zoom_4webserver.txt
www/cyp1b1_infofile.txt
www/cyp1b1_infofile_exprGene_region.txt
www/cyp1b1_res37_rawMatrix.txt
www/cyp1b1_zoom_plus_name_expr.jpg
www/cyp1b1_zoom_plus_name_expr.pdf
www/minimal-cometwebPlot.jpeg
www/server.R www/ui.R
TiphaineCMartin/coMET_original documentation built on May 10, 2017, 4:53 p.m.