Files in luannnguyen/hmfGeneAnnotation
Determines gene amplifications and biallelic losses from HMF pipeline output
DESCRIPTION
NAMESPACE
R/aaa.R
R/calcChromArmPloidies.R
R/convertGeneId.R
R/detGeneStatuses.R
R/misc.R
R/mkDatabases.R
R/mkGeneDiplotypes.R
R/mkMutProfile.R
R/postProcessDiplotypes.R
R/preProcessCnv.R
R/preProcessSnvIndel.R
README.md
doc/README.Rmd
doc/README.md
inst/db/centromere_positions_hg19.txt
inst/db/clinvar.txt.bgz
inst/db/clinvar.txt.bgz.tbi
inst/db/cosmic_cancer_gene_census_20200225.tsv.gz
inst/db/gap.txt.gz
inst/db/hgnc_gene_names.txt.gz
inst/db/human_genes_enst2ensg.txt.gz
inst/misc/cosmic_cancer_gene_census_20200225.bed
inst/misc/cosmic_cancer_gene_census_exons_20200225.bed.gz
inst/misc/genes_chord_paper.bed
inst/scoring/clinvar_scoring.txt
inst/scoring/snpeff_scoring.txt
man/annotateVariantType.Rd
man/calcChromArmPloidies.Rd
man/calcHitScores.Rd
man/detBiallHitType.Rd
man/detBiallStatus.Rd
man/detGeneStatuses.Rd
man/detReadingFrame.Rd
man/ensgToHgncSymbol.Rd
man/extractVcfFields.Rd
man/filterVcf.Rd
man/geneNamesToEnsg.Rd
man/getClinSig.Rd
man/getGeneDiplotypeMaxEff.Rd
man/hello.Rd
man/insColAfter.Rd
man/mkClinvarTxt.Rd
man/mkGeneDiplotypesCnvMut.Rd
man/mkGeneDiplotypesMutMut.Rd
man/mkMutProfileGeneCnv.Rd
man/mkMutProfileSnvIndel.Rd
man/preProcessGeneCnv.Rd
man/retrieveHgncGeneList.Rd
man/write.tsv.Rd
