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 long as the data can be translated to genomic level and for any species.

AuthorTiphaine C. Martin, Thomas Hardiman, Idil Yet, Pei-Chien Tsai, Jordana T. Bell
Date of publicationNone
MaintainerTiphaine Martin <tiphaine.martin@kcl.ac.uk>
LicenseGPL (>= 2)
Version1.6.0
http://epigen.kcl.ac.uk/comet

View on Bioconductor

Man pages

bindingMotifsBiomart_ENSEMBL: Creates a binding motif track from ENSEMBL

check.configVar: Check if all variables have a value related to the functions...

check.configVar.cometlist: Check if all variables have a value related to the function...

check.format.mydata: Check the format of different data

ChIPTF_ENCODE: Creates a TF motif track from ENCODE

chromatinHMMAll_UCSC: Creating multiple chromHMM tracks from the UCSC genome...

chromatinHMMOne_UCSC: Creating one chromHMM track from the UCSC genome browser

chromHMM_RoadMap: Creates a ChromHMM track from a file of RoadMap

chrUCSC2ENSEMBL: Removing "chr" to the chromosome number from UCSC to...

ClinVarCnv_UCSC: Create one track of the genomic positions of variants from...

ClinVarMain_UCSC: Create one track of the genomic positions of variants from...

comet: Visualize EWAS results in a genomic region of interest

comet.list: List the correlations between omic features

coMET-package: visualisation of regional epigenome-wide association scan...

comet.web: Visualize EWAS results in a genomic region of interest with...

compute.cormatrix: Compute the correlation matrix between CpG sites

CoreillCNV_UCSC: Create one track of the genomic positions of CNV in...

COSMIC_UCSC: Create one track of the genomic positions of variants from...

cpgIslands_UCSC: create track CpG Island from UCSC

cpgPvalue: Create a plot of pvalue of CpG with DataTrack of Gviz

create.color.bar: Create color bar of heatmap

create.color.list: Create color list for the main data

create.color.list.large: Create list of colors for the supplementary data

createList.trackUser: Create list of Gviz's tracks from user's data

create.symbol.list: create symbol list for the upper plot in the grid

create.symbol.list.large: Create a list of symblo for the supplementary data

create.tracks.user: Create track from the user data

create.tracks.web: Create tracks for the web page (see cometweb)

datasets: Data sets

dgfootprints_RoadMap: Creates a track of DNA motif positional bias in digital...

DNaseI_FANTOM: Creates a enhancer/promoter track from FANTOM

DNaseI_RoadMap: Creates a promoter/enhancer regions track from a file of...

DNAse_UCSC: Creation of an UCSC's DNase clusters track

draw.legend: Display the legend of the plot

draw.name.genes.web: display the gene names

draw.name.tracks.web: Display names of tracks for web page(see cometweb)

draw.plot.annotation: Display the annotation track from ENSEMBL and UCSC

draw.plot.axis.data: Display the axis data of plot of pvalue

draw.plot.comet: Display the three plots of coMET

draw.plot.comet.nopval: Display the three plots of coMET

draw.plot.comet.web: Display the three plots of coMET for the web version

draw.plot.cormatrix.plot: Display the correlation plot at the bottom of the grid

draw.plot.grid.mydata: Display a plot of pvalue of data from MYDATA.FILE

draw.plot.grid.mydata.large: Display the plot of pvalue of the supplementary data

draw.plot.grid.mydata.names: Display the name of elements defined in DATA.FILE

draw.plot.grid.setup: Set up the grid of plot

draw.plot.linesconnection: Display the connector lines for the probes

draw.plot.mydata.ggbio: plot tracks created by ggbio that you want to visualise

eQTL: Creates a track from a file for eQTL data

eQTL_GTEx: Creates a eQTL track from GTEx

fix.values: Fix and update the values of variables related to main data

fix.values.generic: Fix and update the values of generic variables

fix.values.large: Fix and update the values of supplementary data

GAD_UCSC: Create one track of the genomic positions of variants from...

gcContent_UCSC: Create one track of GC content from UCSC

GeneReviews_UCSC: Create one track of the genomic positions of variants from...

genes_ENSEMBL: Create one track of the genes in the genomic regions of...

genesName_ENSEMBL: Obtain the genes names in the genomic regions of interest...

GWAScatalog_UCSC: Create one track of the genomic positions of variants from...

HiCdata2matrix: Creates a HiC matrix from a file (Rao et al., 2014)

HistoneAll_UCSC: Create multiple tracks of histone modifications from the UCSC...

HistoneOne_UCSC: Create one track of one histone modification profile from the...

imprintedGenes_GTEx: Creates a imprinted genes track from GTEx

interestGenes_ENSEMBL: Create one track of the genes in the genomic regions of...

interestTranscript_ENSEMBL: Create a track of transcripts from ENSEMBL

ISCA_UCSC: Create one track of the genomic positions of variants from...

knownGenes_UCSC: Create a track of known genes from the UCSC genome browser

metQTL: Creates a track from a file for metQTL data

miRNATargetRegionsBiomart_ENSEMBL: Creates a track of miRNA target regions from ENSEMBL

otherRegulatoryRegionsBiomart_ENSEMBL: Creates a track of other regulatory regions from ENSEMBL

printPlot.comet: Create the plot on file from coMet function

printPlot.comet.nopval: Create the plot on file from coMet function

printPlot.comet.web: Display the plot from cometWeb funciton

psiQTL_GTEx: Creates a psiQTL track from GTEx

read.config: Extract the values of variables from configuration file

read.file.cormatrix: Read, compute and extract the values from correlation matrix...

read.file.mydata: Read the files of main data and extract data

read.file.mydata.large: Read the files of supplemantary data and extract data

refGenes_UCSC: Create a track of RefSeq genes from the UCSC genome browser

regulationBiomart_ENSEMBL: Create a regulation track from ENSEMBL

regulatoryEvidenceBiomart_ENSEMBL: Creates a regulatory feature track from ENSEMBL

regulatoryFeaturesBiomart_ENSEMBL: Creates a regulatory feature track from ENSEMBL

regulatorySegmentsBiomart_ENSEMBL: Creates a binding motif track from ENSEMBL

repeatMasker_UCSC: Create one track of the genomic positions of regions from...

retrieve.data: Retrieve the data from configuration file and data files

segmentalDups_UCSC: Create one track of the genomic positions of regions from...

set.image.parameters: Set up the parameters of image

snpBiomart_ENSEMBL: Create a short variation track from ENSEMBL

snpLocations_UCSC: Create a SNP track from UCSC

structureBiomart_ENSEMBL: Create a structural variation track from ENSEMBL

TFBS_FANTOM: Creates a TFBS motif track from FANTOM

transcript_ENSEMBL: Create a track of transcripts from ENSEMBL

xenorefGenes_UCSC: Create a track for xeno-reference genes from the UCSC genome...

Functions

allIG Man page
allIGtrack Man page
allimprintedIG Man page
allimprintedIGtrack Man page
BindingMotifAll Man page
BindingMotifMultiple Man page
bindingMotifsBiomart_ENSEMBL Man page
BindingMotifSingle Man page
bindMotifsBiomartTrackAll Man page
bindMotifsBiomartTrackDouble Man page
bindMotifsBiomartTrackMultiple Man page
bindMotifsBiomartTrackSingle Man page
check.configVar Man page
check.configVarcometlist Man page
check.format.mydata Man page
ChIPTF_ENCODE Man page
chipTFtrack Man page
chromatinHMMAll_UCSC Man page
chromatinHMMOne_UCSC Man page
chromatinHMMRoadMapAll Man page
chromatinHMMRoadMapMultiple Man page
chromatinHMMRoadMapSingle Man page
chromhmmNoPattern Man page
chromhmmPattern Man page
chromHMM_RoadMap Man page
chromHMM_RoadMapAll Man page
chromHMM_RoadMapAllE063 Man page
chromHMM_RoadMapMultiple Man page
chromHMM_RoadMapSingle Man page
chromhmmtrackone Man page
chrUCSC2ENSEMBL Man page
clinCNV Man page
ClinVarCnv_UCSC Man page
clinVariant Man page
ClinVarMain_UCSC Man page
comet Man page
coMET Man page
comet.list Man page
coMET-package Man page
comet.web Man page
compute.cormatrix Man page
CoreillCNV_UCSC Man page
coreilVariant Man page
COSMIC_UCSC Man page
cosmicVariant Man page
cpgIslands_UCSC Man page
cpgIslandtrack Man page
cpgIstrack Man page
cpgPvalue Man page
create.color.bar Man page
create.color.list Man page
create.color.list.large Man page
createList.trackUser Man page
create.symbol.list Man page
create.symbol.list.large Man page
create.tracks.user Man page
create.tracks.web Man page
dgfootprints_RoadMap Man page
dgfootprints_RoadMapSingle Man page
DNaseI_FANTOM Man page
DNaseI_RoadMap Man page
DNaseI_RoadMapSingle Man page
dnasetrack Man page
DNAse_UCSC Man page
draw.legend Man page
draw.name.genes.web Man page
draw.name.tracks.web Man page
draw.plot.annotation Man page
draw.plot.axis.data Man page
draw.plot.comet Man page
draw.plot.comet.nopval Man page
draw.plot.comet.web Man page
draw.plot.cormatrix.plot Man page
draw.plot.grid.mydata Man page
draw.plot.grid.mydata.large Man page
draw.plot.grid.mydata.names Man page
draw.plot.grid.setup Man page
draw.plot.linesconnection Man page
draw.plot.mydata.ggbio Man page
DupTrack Man page
dyaRM Man page
dyaRMtrack Man page
eGTexTrackall Man page
eGTexTrackSNP Man page
enhFANTOMtrack Man page
enhRM Man page
enhRMtrack Man page
eQTL Man page
eQTL_GTEx Man page
eQTLTrackAll Man page
eQTLTrackMultiple Man page
eQTLTrackSingle Man page
fix.values Man page
fix.values.generic Man page
fix.values.large Man page
gadtrack Man page
GAD_UCSC Man page
gcContent_UCSC Man page
gctrack Man page
geneNameEnsembl Man page
GeneReviews_UCSC Man page
geneRtrack Man page
genes_ENSEMBL Man page
genesName_ENSEMBL Man page
genesUcsctrack Man page
genetrack Man page
grtrack Man page
grtrack4eGTex Man page
GWAScatalog_UCSC Man page
gwastrack Man page
HiCdata2matrix Man page
histonalltrack Man page
HistoneAll_UCSC Man page
histoneonetrack Man page
HistoneOne_UCSC Man page
imprintedGenesGTEx Man page
imprintedGenes_GTEx Man page
interestGenes_ENSEMBL Man page
interestgenesENSMBLtrack Man page
interestTranscript_ENSEMBL Man page
interesttransENSMBLtrack Man page
iscatrack Man page
ISCA_UCSC Man page
knownGenes_UCSC Man page
matrix_HiC_Rao Man page
metQTL Man page
metQTLTrackAll Man page
metQTLTrackMultiple Man page
metQTLTrackSingle Man page
miRNATargetRegionsBiomart_ENSEMBL Man page
miRNATargetRegionsBiomartTrack Man page
otherRegulatoryRegions_ENSEMBL Man page
otherRegulatoryRegionsTrackAll Man page
OtherRegulatoryRegionsTrackAll Man page
otherRegulatoryRegionsTrackSingle Man page
OtherRegulatoryRegionsTrackSingle Man page
PancreasIG Man page
PancreasIGtrack Man page
PancreasimprintedIG Man page
PancreasimprintedIGtrack Man page
printPlot.comet Man page
printPlot.comet.nopval Man page
printPlot.comet.web Man page
promRMtrack Man page
promRMtrackE063 Man page
psiGTex Man page
psiGTexTrackall Man page
psiGTexTrackSNP Man page
psiQTL_GTEx Man page
read.config Man page
read.file.cormatrix Man page
read.file.mydata Man page
read.file.mydata.large Man page
refGenes_UCSC Man page
regulationBiomart_ENSEMBL Man page
regulationENSEMBLtrack Man page
regulatoryEvidenceBiomart_ENSEMBL Man page
regulatoryEvidenceBiomartTrackAll Man page
RegulatoryEvidenceBiomartTrackAll Man page
regulatoryEvidenceBiomartTrackMultiple Man page
RegulatoryEvidenceBiomartTrackMultiple Man page
regulatoryEvidenceBiomartTrackSingle Man page
RegulatoryEvidenceBiomartTrackSingle Man page
regulatoryFeaturesBiomart_ENSEMBL Man page
regulatoryFeaturesBiomartTrackAll Man page
RegulatoryFeaturesBiomartTrackAll Man page
regulatoryFeaturesBiomartTrackMultiple Man page
RegulatoryFeaturesBiomartTrackMultiple Man page
regulatoryFeaturesBiomartTrackSingle Man page
RegulatoryFeaturesBiomartTrackSingle Man page
regulatorySegmentsBiomart_ENSEMBL Man page
regulatorySegmentsBiomartTrackAll Man page
RegulatorySegmentsBiomartTrackAll Man page
regulatorySegmentsBiomartTrackMultiple Man page
RegulatorySegmentsBiomartTrackMultiple Man page
regulatorySegmentsBiomartTrackSingle Man page
RegulatorySegmentsBiomartTrackSingle Man page
repeatMaskerTrack Man page
repeatMasker_UCSC Man page
retrieve.data Man page
rmtrack Man page
segmentalDups_UCSC Man page
set.image.parameters Man page
snpBiomart_ENSEMBL Man page
snpLocations_UCSC Man page
snptrack Man page
snpUCSCtrack Man page
StomachIG Man page
StomachIGtrack Man page
structureBiomart_ENSEMBL Man page
strutrack Man page
TFBS_FANTOM Man page
tfbsFANTOMtrack Man page
transcript_ENSEMBL Man page
transENSMBLtrack Man page
xenogenestrack Man page
xenorefGenes_UCSC Man page

Files

coMET/DESCRIPTION
coMET/LICENSE
coMET/NAMESPACE
coMET/NEWS
coMET/R
coMET/R/AnalyseFile.R coMET/R/BiofeatureGraphics.R coMET/R/DrawPlot.R coMET/R/GeneralMethodComet.R coMET/R/comet.R coMET/R/cometWeb.R coMET/R/cometlist.R
coMET/README.md
coMET/build
coMET/build/vignette.rds
coMET/data
coMET/data/BindingMotifAll.rda
coMET/data/BindingMotifMultiple.rda
coMET/data/BindingMotifSingle.rda
coMET/data/ClinVarCnvTrack.rda
coMET/data/CoreillCNVTrack.rda
coMET/data/DNaseI_RoadMapSingle.rda
coMET/data/DupTrack.rda
coMET/data/GWASTrack.rda
coMET/data/GeneReviewTrack.rda
coMET/data/GeneReviewsTrack.rda
coMET/data/ISCAtrack.rda
coMET/data/ISCAtrack_Grch38.rda
coMET/data/OtherRegulatoryRegionsAll.rda
coMET/data/OtherRegulatoryRegionsSingle.rda
coMET/data/PancreasIG.rda
coMET/data/PancreasIGtrack.rda
coMET/data/PancreasimprintedIG.rda
coMET/data/PancreasimprintedIGtrack.rda
coMET/data/RegulatoryEvidenceBiomartAll.rda
coMET/data/RegulatoryEvidenceBiomartMultiple.rda
coMET/data/RegulatoryEvidenceBiomartSingle.rda
coMET/data/RegulatoryFeaturesBiomartAll.rda
coMET/data/RegulatoryFeaturesBiomartMultiple.rda
coMET/data/RegulatoryFeaturesBiomartSingle.rda
coMET/data/RegulatorySegmentsBiomartAll.rda
coMET/data/RegulatorySegmentsBiomartMultiple.rda
coMET/data/RegulatorySegmentsBiomartSingle.rda
coMET/data/SegmentalDupsUCSC.rda
coMET/data/StomachIG.rda
coMET/data/StomachIGtrack.rda
coMET/data/allIG.rda
coMET/data/allIGtrack.rda
coMET/data/allimprintedIG.rda
coMET/data/allimprintedIGtrack.rda
coMET/data/bindMotifsBiomartTrackAll.rda
coMET/data/bindMotifsBiomartTrackMultiple.rda
coMET/data/bindMotifsBiomartTrackSingle.rda
coMET/data/bindingMotifsBiomartAll.rda
coMET/data/bindingMotifsBiomartMultiple.rda
coMET/data/bindingMotifsBiomartSingle.rda
coMET/data/chipTFtrack.rda
coMET/data/chipTFtrack_old.rda
coMET/data/chromHMM_RoadMapAll.rda
coMET/data/chromHMM_RoadMapAllE063.rda
coMET/data/chromHMM_RoadMapMultiple.rda
coMET/data/chromHMM_RoadMapSingle.rda
coMET/data/chromatinHMMRoadMapAll.rda
coMET/data/chromatinHMMRoadMapMultiple.rda
coMET/data/chromatinHMMRoadMapSingle.rda
coMET/data/chromhmmNoPattern.rda
coMET/data/chromhmmPattern.rda
coMET/data/chromhmmtrackone.rda
coMET/data/clinVarMaintrack.rda
coMET/data/coreilVarianttrack.rda
coMET/data/cosmicVarianttrack.rda
coMET/data/cpgIslandsUCSC.rda
coMET/data/cpgIslandtrack.rda
coMET/data/datalist
coMET/data/dgfootprints_RoadMapSingle.rda
coMET/data/dnasetrack.rda
coMET/data/dyaRM.rda
coMET/data/dyaRMtrack.rda
coMET/data/eGTexTrackSNP.rda
coMET/data/eGTexTrackall.rda
coMET/data/eQTLAll.rda
coMET/data/eQTLMultiple.rda
coMET/data/eQTLSingle.rda
coMET/data/eQTLTrackAll.rda
coMET/data/eQTLTrackMultiple.rda
coMET/data/eQTLTrackSingle.rda
coMET/data/enhFANTOMtrack.rda
coMET/data/enhRM.rda
coMET/data/enhRMtrack.rda
coMET/data/gadtrack.rda
coMET/data/gcContent.rda
coMET/data/gctrack.rda
coMET/data/geneENSEMBLtrack.rda
coMET/data/geneNameEnsembl.rda
coMET/data/genesENSEMBL.rda
coMET/data/genesGencodetrack.rda
coMET/data/genesNameENSEMBL.rda
coMET/data/genesUcsctrack.rda
coMET/data/genetrack4RM.rda
coMET/data/genetrack4psiGTEX.rda
coMET/data/grtrack4eGTex.rda
coMET/data/histonalltrack.rda
coMET/data/histoneonetrack.rda
coMET/data/imprintedGenesGTEx.rda
coMET/data/interestGenesENSEMBL.rda
coMET/data/interestTranscriptENSEMBL.rda
coMET/data/interestgenesENSMBLtrack.rda
coMET/data/interesttransENSMBLtrack.rda
coMET/data/knownGenesUCSC.rda
coMET/data/matrix_HiC_Rao.rda
coMET/data/metQTLSingle.rda
coMET/data/metQTLTrackAll.rda
coMET/data/metQTLTrackMultiple.rda
coMET/data/metQTLTrackSingle.rda
coMET/data/miRNATargetRegionsBiomart.rda
coMET/data/miRNATargetRegionsBiomartTrack.rda
coMET/data/otherRegulatoryRegionsTrackAll.rda
coMET/data/otherRegulatoryRegionsTrackSingle.rda
coMET/data/promRMtrack.rda
coMET/data/promRMtrackE063.rda
coMET/data/psiGTex.rda
coMET/data/psiGTexTrackSNP.rda
coMET/data/psiGTexTrackall.rda
coMET/data/refGenesUCSC.rda
coMET/data/regulationENSEMBLtrack.rda
coMET/data/regulatoryEvidenceBiomartTrackAll.rda
coMET/data/regulatoryEvidenceBiomartTrackMultiple.rda
coMET/data/regulatoryEvidenceBiomartTrackSingle.rda
coMET/data/regulatoryFeaturesBiomartTrackAll.rda
coMET/data/regulatoryFeaturesBiomartTrackMultiple.rda
coMET/data/regulatoryFeaturesBiomartTrackSingle.rda
coMET/data/regulatorySegmentsBiomartTrackAll.rda
coMET/data/regulatorySegmentsBiomartTrackMultiple.rda
coMET/data/regulatorySegmentsBiomartTrackSingle.rda
coMET/data/repeatMaskerTrack.rda
coMET/data/snpBiomart.rda
coMET/data/snpBiomarttrack.rda
coMET/data/snpUCSCtrack.rda
coMET/data/snptrack.rda
coMET/data/strucBiomarttrack.rda
coMET/data/structureBiomart.rda
coMET/data/tfbsFANTOMtrack.rda
coMET/data/transENSMBLtrack.rda
coMET/data/xenogenestrack.rda
coMET/data/xenorefGenesUCSC.rda
coMET/inst
coMET/inst/CITATION
coMET/inst/doc
coMET/inst/doc/coMET.R
coMET/inst/doc/coMET.Rnw
coMET/inst/doc/coMET.pdf
coMET/inst/extdata
coMET/inst/extdata/JpegTables
coMET/inst/extdata/JpegTables/BindingMotifsBiomart.jpg
coMET/inst/extdata/JpegTables/ChromHMM.jpg
coMET/inst/extdata/JpegTables/ChromHMM_UCSC.jpg
coMET/inst/extdata/JpegTables/ChromHMM_coMET.jpg
coMET/inst/extdata/JpegTables/ISCATrack.jpg
coMET/inst/extdata/JpegTables/ISCATrack_old.jpg
coMET/inst/extdata/JpegTables/OtherRegulatoryRegions.jpg
coMET/inst/extdata/JpegTables/RegulatoryElementsENSEMBL.jpg
coMET/inst/extdata/JpegTables/RegulatoryEvidence_1.jpg
coMET/inst/extdata/JpegTables/RegulatoryEvidence_2.jpg
coMET/inst/extdata/JpegTables/RegulatoryEvidence_3.jpg
coMET/inst/extdata/JpegTables/RegulatoryFeaturesBiomart.jpg
coMET/inst/extdata/JpegTables/RegulatorySegmentsBiomart.jpg
coMET/inst/extdata/JpegTables/RoadMap15_RoadMap.jpg
coMET/inst/extdata/JpegTables/RoadMap18_RoadMap.jpg
coMET/inst/extdata/JpegTables/RoadMap18_coMET.jpg
coMET/inst/extdata/JpegTables/RoadMap25_RoadMap.jpg
coMET/inst/extdata/JpegTables/RoadMap25_coMET.jpg
coMET/inst/extdata/JpegTables/bindingMotifBiomart.jpg
coMET/inst/extdata/JpegTables/eQTL.jpg
coMET/inst/extdata/JpegTables/metQTL.jpg
coMET/inst/extdata/JpegTables/structureBiomart.jpg
coMET/inst/extdata/config_cyp1b1_zoom.txt
coMET/inst/extdata/config_cyp1b1_zoom_4comet.txt
coMET/inst/extdata/config_cyp1b1_zoom_4cometnopval.txt
coMET/inst/extdata/config_cyp1b1_zoom_4cometnopval_Grch38.txt
coMET/inst/extdata/config_cyp1b1_zoom_4nomatrix.txt
coMET/inst/extdata/config_cyp1b1_zoom_4nomatrix_Grch38.txt
coMET/inst/extdata/config_cyp1b1_zoom_4webserver.txt
coMET/inst/extdata/config_cyp1b1_zoom_4webserver_Grch38.txt
coMET/inst/extdata/config_gata55_larger_article.txt
coMET/inst/extdata/config_gata55_larger_article_rev.txt
coMET/inst/extdata/cyp1b1_infofile.bed
coMET/inst/extdata/cyp1b1_infofile.txt
coMET/inst/extdata/cyp1b1_infofile_Grch38.txt
coMET/inst/extdata/cyp1b1_infofile_bed.txt
coMET/inst/extdata/cyp1b1_infofile_bed_v2.bed
coMET/inst/extdata/cyp1b1_infofile_bed_v2.txt
coMET/inst/extdata/cyp1b1_infofile_bed_v2_hg38.bed
coMET/inst/extdata/cyp1b1_infofile_bed_v3.bed
coMET/inst/extdata/cyp1b1_infofile_bed_v3.txt
coMET/inst/extdata/cyp1b1_infofile_bed_v3_hg38.bed
coMET/inst/extdata/cyp1b1_infofile_exprGene_region.txt
coMET/inst/extdata/cyp1b1_infofile_exprGene_region_Grch38.txt
coMET/inst/extdata/cyp1b1_infofile_exprGene_region_v2.csv
coMET/inst/extdata/cyp1b1_res37_cormatrix_list_BH05.txt
coMET/inst/extdata/cyp1b1_res37_rawMatrix.txt
coMET/inst/extdata/cyp1b1_zoom_plus_name_expr.pdf
coMET/inst/extdata/datalist
coMET/inst/extdata/gata4_55probes_info.txt
coMET/inst/extdata/gata4_55probes_rawMatrix.txt
coMET/inst/extdata/gata4_55probes_residuals.txt
coMET/inst/extdata/gata4_95probes_info.txt
coMET/inst/extdata/gata_comet_55probes_large_article.eps
coMET/inst/extdata/gata_comet_55probes_large_article_gene.eps
coMET/inst/extdata/gata_comet_55probes_large_article_rev.eps
coMET/inst/unitTests
coMET/inst/unitTests/ChangeLog.txt
coMET/inst/unitTests/Citation.txt
coMET/inst/unitTests/test_chrUCSC2ENSEMBL.R
coMET/man
coMET/man/COSMIC_UCSC.Rd coMET/man/ChIPTF_ENCODE.Rd coMET/man/ClinVarCnv_UCSC.Rd coMET/man/ClinVarMain_UCSC.Rd coMET/man/CoreillCNV_UCSC.Rd coMET/man/DNAse_UCSC.Rd coMET/man/DNaseI_FANTOM.Rd coMET/man/DNaseI_RoadMap.Rd coMET/man/GAD_UCSC.Rd coMET/man/GWAScatalog_UCSC.Rd coMET/man/GeneReviews_UCSC.Rd coMET/man/HiCdata2matrix.Rd coMET/man/HistoneAll_UCSC.Rd coMET/man/HistoneOne_UCSC.Rd coMET/man/ISCA_UCSC.Rd coMET/man/TFBS_FANTOM.Rd coMET/man/bindingMotifsBiomart_ENSEMBL.Rd coMET/man/check.configVar.Rd coMET/man/check.configVar.cometlist.Rd coMET/man/check.format.mydata.Rd coMET/man/chrUCSC2ENSEMBL.Rd coMET/man/chromHMM_RoadMap.Rd coMET/man/chromatinHMMAll_UCSC.Rd coMET/man/chromatinHMMOne_UCSC.Rd coMET/man/coMET-package.Rd coMET/man/comet.Rd coMET/man/comet.list.Rd coMET/man/comet.web.Rd coMET/man/compute.cormatrix.Rd coMET/man/cpgIslands_UCSC.Rd coMET/man/cpgPvalue.Rd coMET/man/create.color.bar.Rd coMET/man/create.color.list.Rd coMET/man/create.color.list.large.Rd coMET/man/create.symbol.list.Rd coMET/man/create.symbol.list.large.Rd coMET/man/create.tracks.user.Rd coMET/man/create.tracks.web.Rd coMET/man/createList.trackUser.Rd coMET/man/datasets.Rd coMET/man/dgfootprints_RoadMap.Rd coMET/man/draw.legend.Rd coMET/man/draw.name.genes.web.Rd coMET/man/draw.name.tracks.web.Rd coMET/man/draw.plot.annotation.Rd coMET/man/draw.plot.axis.data.Rd coMET/man/draw.plot.comet.Rd coMET/man/draw.plot.comet.nopval.Rd coMET/man/draw.plot.comet.web.Rd coMET/man/draw.plot.cormatrix.plot.Rd coMET/man/draw.plot.grid.mydata.Rd coMET/man/draw.plot.grid.mydata.large.Rd coMET/man/draw.plot.grid.mydata.names.Rd coMET/man/draw.plot.grid.setup.Rd coMET/man/draw.plot.linesconnection.Rd coMET/man/draw.plot.mydata.ggbio.Rd coMET/man/eQTL.Rd coMET/man/eQTL_GTEx.Rd coMET/man/fix.values.Rd coMET/man/fix.values.generic.Rd coMET/man/fix.values.large.Rd coMET/man/gcContent_UCSC.Rd coMET/man/genesName_ENSEMBL.Rd coMET/man/genes_ENSEMBL.Rd coMET/man/imprintedGenes_GTEx.Rd coMET/man/interestGenes_ENSEMBL.Rd coMET/man/interestTranscript_ENSEMBL.Rd coMET/man/knownGenes_UCSC.Rd coMET/man/metQTL.Rd coMET/man/miRNATargetRegionsBiomart_ENSEMBL.Rd coMET/man/otherRegulatoryRegionsBiomart_ENSEMBL.Rd coMET/man/printPlot.comet.Rd coMET/man/printPlot.comet.nopval.Rd coMET/man/printPlot.comet.web.Rd coMET/man/psiQTL_GTEx.Rd coMET/man/read.config.Rd coMET/man/read.file.cormatrix.Rd coMET/man/read.file.mydata.Rd coMET/man/read.file.mydata.large.Rd coMET/man/refGenes_UCSC.Rd coMET/man/regulationBiomart_ENSEMBL.Rd coMET/man/regulatoryEvidenceBiomart_ENSEMBL.Rd coMET/man/regulatoryFeaturesBiomart_ENSEMBL.Rd coMET/man/regulatorySegmentsBiomart_ENSEMBL.Rd coMET/man/repeatMasker_UCSC.Rd coMET/man/retrieve.data.Rd coMET/man/segmentalDups_UCSC.Rd coMET/man/set.image.parameters.Rd coMET/man/snpBiomart_ENSEMBL.Rd coMET/man/snpLocations_UCSC.Rd coMET/man/structureBiomart_ENSEMBL.Rd coMET/man/transcript_ENSEMBL.Rd coMET/man/xenorefGenes_UCSC.Rd
coMET/tests
coMET/tests/runTests.R
coMET/vignettes
coMET/vignettes/biblio.bib
coMET/vignettes/coMET.Rnw
coMET/www
coMET/www/Readme.md
coMET/www/comet
coMET/www/comet/DESCRIPTION
coMET/www/comet/server.R
coMET/www/comet/ui.R
coMET/www/cometpdf
coMET/www/cometpdf/DESCRIPTION
coMET/www/cometpdf/server.R
coMET/www/cometpdf/ui.R
coMET/www/conf
coMET/www/conf/shiny-server.conf
coMET/www/config_cyp1b1_zoom.txt
coMET/www/config_cyp1b1_zoom_4webserver.txt
coMET/www/cyp1b1_infofile.txt
coMET/www/cyp1b1_infofile_exprGene_region.txt
coMET/www/cyp1b1_res37_rawMatrix.txt
coMET/www/cyp1b1_zoom_plus_name_expr.jpg
coMET/www/cyp1b1_zoom_plus_name_expr.pdf
coMET/www/cyp1b1info.txt
coMET/www/cyp1b1info_expr_reduce_region.txt
coMET/www/cyp1b1res_37.txt
coMET/www/minimal-cometwebPlot.jpeg

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