Name Mode Size
..
BindingMotifAll.rda 100644 2 kb
BindingMotifMultiple.rda 100644 2 kb
BindingMotifSingle.rda 100644 2 kb
ClinVarCnvTrack.rda 100644 1 kb
CoreillCNVTrack.rda 100644 1 kb
DNaseI_RoadMapSingle.rda 100644 154 kb
DupTrack.rda 100644 1 kb
GWASTrack.rda 100644 1 kb
GeneReviewTrack.rda 100644 2 kb
GeneReviewsTrack.rda 100644 2 kb
ISCAtrack.rda 100644 1 kb
ISCAtrack_Grch38.rda 100644 1 kb
OtherRegulatoryRegionsAll.rda 100644 8 kb
OtherRegulatoryRegionsSingle.rda 100644 2 kb
PancreasIG.rda 100644 76 kb
PancreasIGtrack.rda 100644 76 kb
PancreasimprintedIG.rda 100644 1 kb
PancreasimprintedIGtrack.rda 100644 1 kb
RegulatoryEvidenceBiomartAll.rda 100644 13 kb
RegulatoryEvidenceBiomartMultiple.rda 100644 7 kb
RegulatoryEvidenceBiomartSingle.rda 100644 6 kb
RegulatoryFeaturesBiomartAll.rda 100644 2 kb
RegulatoryFeaturesBiomartMultiple.rda 100644 2 kb
RegulatoryFeaturesBiomartSingle.rda 100644 1 kb
RegulatorySegmentsBiomartAll.rda 100644 2 kb
RegulatorySegmentsBiomartMultiple.rda 100644 2 kb
RegulatorySegmentsBiomartSingle.rda 100644 2 kb
SegmentalDupsUCSC.rda 100644 1 kb
StomachIG.rda 100644 1 kb
StomachIGtrack.rda 100644 1 kb
allIG.rda 100644 76 kb
allIGtrack.rda 100644 76 kb
allimprintedIG.rda 100644 76 kb
allimprintedIGtrack.rda 100644 76 kb
bindMotifsBiomartTrackAll.rda 100644 2 kb
bindMotifsBiomartTrackMultiple.rda 100644 2 kb
bindMotifsBiomartTrackSingle.rda 100644 2 kb
bindingMotifsBiomartAll.rda 100644 2 kb
bindingMotifsBiomartMultiple.rda 100644 2 kb
bindingMotifsBiomartSingle.rda 100644 2 kb
chipTFtrack.rda 100755 5 kb
chipTFtrack_old.rda 100644 5 kb
chromHMM_RoadMapAll.rda 100644 2 kb
chromHMM_RoadMapAllE063.rda 100644 2 kb
chromHMM_RoadMapMultiple.rda 100644 2 kb
chromHMM_RoadMapSingle.rda 100644 2 kb
chromatinHMMRoadMapAll.rda 100644 2 kb
chromatinHMMRoadMapMultiple.rda 100644 2 kb
chromatinHMMRoadMapSingle.rda 100644 2 kb
chromhmmNoPattern.rda 100644 3 kb
chromhmmPattern.rda 100644 2 kb
chromhmmtrackone.rda 100644 2 kb
clinVarMaintrack.rda 100644 2 kb
coreilVarianttrack.rda 100644 1 kb
cosmicVarianttrack.rda 100644 2 kb
cpgIslandsUCSC.rda 100644 2 kb
cpgIslandtrack.rda 100644 1 kb
datalist 100644 4 kb
dgfootprints_RoadMapSingle.rda 100644 85 kb
dnasetrack.rda 100644 1 kb
dyaRM.rda 100644 132 kb
dyaRMtrack.rda 100644 1 kb
eGTexTrackSNP.rda 100644 2 kb
eGTexTrackall.rda 100644 2 kb
eQTLAll.rda 100644 2 kb
eQTLMultiple.rda 100644 2 kb
eQTLSingle.rda 100644 2 kb
eQTLTrackAll.rda 100644 2 kb
eQTLTrackMultiple.rda 100644 2 kb
eQTLTrackSingle.rda 100644 2 kb
enhFANTOMtrack.rda 100644 354 kb
enhRM.rda 100644 1,274 kb
enhRMtrack.rda 100644 1,274 kb
gadtrack.rda 100644 1 kb
gcContent.rda 100644 6 kb
gctrack.rda 100644 6 kb
geneENSEMBLtrack.rda 100644 79 kb
geneNameEnsembl.rda 100644 0 kb
genesENSEMBL.rda 100644 85 kb
genesGencodetrack.rda 100755 6 kb
genesNameENSEMBL.rda 100644 0 kb
genesUcsctrack.rda 100644 2 kb
genetrack4RM.rda 100644 76 kb
genetrack4psiGTEX.rda 100644 76 kb
grtrack4eGTex.rda 100644 2,286 kb
histonalltrack.rda 100644 2 kb
histoneonetrack.rda 100644 1 kb
imprintedGenesGTEx.rda 100644 9 kb
interestGenesENSEMBL.rda 100644 85 kb
interestTranscriptENSEMBL.rda 100644 86 kb
interestgenesENSEMBLtrack.rda 100644 75 kb
interestgenesENSMBLtrack.rda 100644 108 kb
interesttransENSMBLtrack.rda 100644 109 kb
knownGenesUCSC.rda 100644 2 kb
matrix_HiC_Rao.rda 100644 0 kb
metQTLSingle.rda 100644 1 kb
metQTLTrackAll.rda 100644 2 kb
metQTLTrackMultiple.rda 100644 2 kb
metQTLTrackSingle.rda 100644 1 kb
miRNATargetRegionsBiomart.rda 100644 2 kb
miRNATargetRegionsBiomartTrack.rda 100644 3 kb
otherRegulatoryRegionsTrackAll.rda 100644 8 kb
otherRegulatoryRegionsTrackSingle.rda 100644 2 kb
promRMtrack.rda 100644 197 kb
promRMtrackE063.rda 100644 154 kb
psiGTex.rda 100644 9 kb
psiGTexTrackSNP.rda 100644 8 kb
psiGTexTrackall.rda 100644 9 kb
refGenesUCSC.rda 100644 2 kb
regulationENSEMBLtrack.rda 100644 2 kb
regulatoryEvidenceBiomartTrackAll.rda 100644 4 kb
regulatoryEvidenceBiomartTrackMultiple.rda 100644 4 kb
regulatoryEvidenceBiomartTrackSingle.rda 100644 3 kb
regulatoryFeaturesBiomartTrackAll.rda 100644 2 kb
regulatoryFeaturesBiomartTrackMultiple.rda 100644 2 kb
regulatoryFeaturesBiomartTrackSingle.rda 100644 1 kb
regulatorySegmentsBiomartTrackAll.rda 100644 2 kb
regulatorySegmentsBiomartTrackMultiple.rda 100644 2 kb
regulatorySegmentsBiomartTrackSingle.rda 100644 2 kb
repeatMaskerTrack.rda 100644 2 kb
snpBiomart.rda 100644 2 kb
snpBiomarttrack.rda 100644 2 kb
snpUCSCtrack.rda 100644 5 kb
snptrack.rda 100644 2 kb
strucBiomarttrack.rda 100644 2 kb
structureBiomart.rda 100644 2 kb
tfbsFANTOMtrack.rda 100644 1 kb
transENSMBLtrack.rda 100644 85 kb
xenogenestrack.rda 100644 2 kb
xenorefGenesUCSC.rda 100644 2 kb
README.md
coMET ===== ##Overview The coMET package is a web-based plotting tool and R-based package to visualize different genome-wide association scans such as EWAS (epigenome-wide association scan) results in a genomic region of interest. coMET provides a plot of the EWAS association signal and visualisation of the methylation correlation between CpG sites (co-methylation). The coMET package also provides the option to annotate the region using functional genomic information, including both user-defined features and pre-selected features based on such as ENSEMBL (http://www.ensembl.org/index.html) , the Encode project, ROADMAP epigenomics projects http://www.roadmapepigenomics.org/ , The Genotype-Tissue Expression (GTEx) project http://www.gtexportal.org/ and FANTOM5 project https://genome.ucsc.edu/ and annotation tracks from UCSC Genome Browser website. The plot can be customized with different parameters, such as plot labels, colours, symbols, heatmap colour scheme, significance thresholds, and including reference CpG sites. Finally, the tool can also be applied to display the correlation patterns of other genomic data and any species, e.g. gene expression array data. ##coMET webservice The webservice is the pre-formated web service of coMET with a reduction of parameters availlable. Go to : http://www.epigen.kcl.ac.uk/comet or directly one of instance: http://comet.epigen.kcl.ac.uk:3838/coMET/ ##Developpers coMET is developed by Tiphaine C. Martin in collaboration with Idil Erte, Pei-Chien Tsai, Jordana T.Bell, Department of Twin Research, Kings College London. ##Cite Martin, T.C., Erte, I., Tsai, P-C., Bell and J.T. (2015). coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns. BMC Bioinformatics. Martin, T.C, Erte, I, Tsai, P-C, Bell, J.T.,coMET: an R plotting package to visualize regional plots of epigenome-wide association scan results, QC14, 2014. ##Contacts For any question, you can send an email to Tiphaine Martin (tiphaine.martin at kcl.ac.uk) and Jordana Bell (jordana.bell at kcl.ac.uk) ##More information Go to the website of Epigenetic group of Department of Twin Research : http://epigen.kcl.ac.uk/comet Go to the help of coMET webservice : http://comet.epigen.kcl.ac.uk:3838/coMET/ Go to the webiste of Department of Twin Research : http://www.twinsuk.ac.uk/