coMET-package |
visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns (and also for other omic-WAS) |
chromatinHMMAll |
Creating multiple chromHMM tracks from the UCSC genome browser |
chromatinHMMOne |
Creating one chromHMM track from the UCSC genome browser |
chrUCSC2ENSEMBL |
Removing "chr" to the chromosome number from UCSC to transform it to ENSEMBL chromosome format |
ClinVarCnvTrack |
Create one track of the genomic positions of variants from the ClinVar database (CNV only) |
ClinVarMainTrack |
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 |
CoreillCNVTrack |
Create one track of the genomic positions of CNV in chromosomal aberration and inherited disorders from the NIGMS Human Genetic Cell Repository data |
COSMICTrack |
Create one track of the genomic positions of variants from COSMIC |
cpgIslandsUCSC |
create track CpG Island from UCSC |
DNAseUCSC |
Creation of an UCSC's DNase clusters track |
GADTrack |
Create one track of the genomic positions of variants from the Genetic Association Database (GAD) |
gcContent |
Create one track of GC content from UCSC |
GeneReviewsTrack |
Create one track of the genomic positions of variants from GeneReviews |
genesENSEMBL |
Create one track of the genes in the genomic regions of interest from EMSEMBL |
genesNameENSEMBL |
Obtain the genes names in the genomic regions of interest from ENSEMBL |
GWASTrack |
Create one track of the genomic positions of variants from the GWAS catalog |
HistoneAll |
Create multiple tracks of histone modifications from the UCSC genome browser |
HistoneOne |
Create one track of one histone modification profile from the UCSC genome browser |
ISCATrack |
Create one track of the genomic positions of variants from ISCA |
knownGenesUCSC |
Create a track of known genes from the UCSC genome browser |
regulationBiomart |
Create a regulation track from ENSEMBL |
RepeatMaskerTrack |
Create one track of the genomic positions of regions from RepeatMaskerTrack |
snpBiomart |
Create a short variation track from ENSEMBL |
snpLocationsUCSC |
Create a SNP track from UCSC |
structureBiomart |
Create a structural variation track from ENSEMBL |
transcriptENSEMBL |
Create a track of transcripts from ENSEMBL |