coMET-package | visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns (and also for other omic-WAS) |
bindingMotifsBiomart_ENSEMBL | Creates a binding motif track from ENSEMBL |
ChIPTF_ENCODE | Creates a TF motif track from ENCODE |
chromatinHMMAll_UCSC | Creating multiple chromHMM tracks from the UCSC genome browser |
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 transform it to ENSEMBL chromosome format |
ClinVarCnv_UCSC | Create one track of the genomic positions of variants from the ClinVar database (CNV only) |
ClinVarMain_UCSC | Create one track of the genomic positions of variants from the ClinVar database (variants only) |
coMET | visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns (and also for other omic-WAS) |
comet | Visualize EWAS results in a genomic region of interest |
comet.list | List the correlations between omic features |
comet.web | Visualize EWAS results in a genomic region of interest with predefined annotation tracks |
CoreillCNV_UCSC | Create one track of the genomic positions of CNV in chromosomal aberration and inherited disorders from the NIGMS Human Genetic Cell Repository data |
COSMIC_UCSC | Create one track of the genomic positions of variants from COSMIC [obselete] |
cpgIslands_UCSC | create track CpG Island from UCSC |
dgfootprints_RoadMap | Creates a track of DNA motif positional bias in digital genomic Footprinting Sites (DGFP) from a file of RoadMap |
DNaseI_FANTOM | Creates a enhancer/promoter track from FANTOM |
DNaseI_RoadMap | Creates a promoter/enhancer regions track from a file of RoadMap |
DNAse_UCSC | Creation of an UCSC's DNase clusters track |
eQTL | Creates a track from a file for eQTL data |
eQTL_GTEx | Creates a eQTL track from GTEx |
GAD_UCSC | Create one track of the genomic positions of variants from the Genetic Association Database (GAD) |
gcContent_UCSC | Create one track of GC content from UCSC |
GeneReviews_UCSC | Create one track of the genomic positions of variants from GeneReviews |
genesName_ENSEMBL | Obtain the genes names in the genomic regions of interest from ENSEMBL |
genes_ENSEMBL | Create one track of the genes in the genomic regions of interest from EMSEMBL |
GWAScatalog_UCSC | Create one track of the genomic positions of variants from the GWAS catalog |
HiCdata2matrix | Creates a HiC matrix from a file (Rao et al., 2014) |
HistoneAll_UCSC | Create multiple tracks of histone modifications from the UCSC genome browser |
HistoneOne_UCSC | Create one track of one histone modification profile from the UCSC genome browser |
imprintedGenes_GTEx | Creates a imprinted genes track from GTEx |
interestGenes_ENSEMBL | Create one track of the genes in the genomic regions of interest from EMSEMBL |
interestTranscript_ENSEMBL | Create a track of transcripts from ENSEMBL |
ISCA_UCSC | Create one track of the genomic positions of variants from ISCA [obselete database] |
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 |
psiQTL_GTEx | Creates a psiQTL track from GTEx |
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 [obselete] |
repeatMasker_UCSC | Create one track of the genomic positions of regions from repeatMasker_UCSC |
segmentalDups_UCSC | Create one track of the genomic positions of regions from segmentalDups_UCSC |
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 |