Files in rcastelo/GenomicScores

Infrastructure to work with genomewide position-specific scores

.Rbuildignore

.github/workflows/check-bioc.yml

.gitignore

DESCRIPTION

NAMESPACE

NEWS

R/AllClasses.R R/AllGeneric.R R/availableGScores.R R/getGScores.R R/makeGScoresPackage.R R/methods-GScores.R R/methods-shinyApp.R R/utils.R README.md

inst/CITATION

inst/extdata/AlphaMissense.v2023.hg38.chr20.rds

inst/extdata/AlphaMissense.v2023.hg38.chr21.rds

inst/extdata/AlphaMissense.v2023.hg38.chr22.rds

inst/extdata/GScoresResourcesMetadata.csv

inst/extdata/avgs.rds

inst/extdata/avgsbmi.rds

inst/extdata/cadd.v1.6.hg38.chr20.rds

inst/extdata/cadd.v1.6.hg38.chr21.rds

inst/extdata/cadd.v1.6.hg38.chr22.rds

inst/extdata/gwcgr_chr20-22_151123.rds

inst/extdata/metadata_AlphaMissense.v2023.hg19.csv

inst/extdata/metadata_AlphaMissense.v2023.hg38.csv

inst/extdata/metadata_MCAP.v1.0.hg19.csv

inst/extdata/metadata_cadd.v1.3.hg19.csv

inst/extdata/metadata_cadd.v1.6.hg19.csv

inst/extdata/metadata_cadd.v1.6.hg38.csv

inst/extdata/metadata_fitCons.UCSC.hg19.csv

inst/extdata/metadata_linsight.UCSC.hg19.csv

inst/extdata/metadata_phastCons100way.UCSC.hg19.csv

inst/extdata/metadata_phastCons100way.UCSC.hg38.csv

inst/extdata/metadata_phastCons27way.UCSC.dm6.csv

inst/extdata/metadata_phastCons30way.UCSC.hg38.csv

inst/extdata/metadata_phastCons35way.UCSC.mm39.csv

inst/extdata/metadata_phastCons46wayPlacental.UCSC.hg19.csv

inst/extdata/metadata_phastCons46wayPrimates.UCSC.hg19.csv

inst/extdata/metadata_phastCons60way.UCSC.mm10.csv

inst/extdata/metadata_phastCons7way.UCSC.hg38.csv

inst/extdata/metadata_phyloP100way.UCSC.hg19.csv

inst/extdata/metadata_phyloP100way.UCSC.hg38.csv

inst/extdata/metadata_phyloP35way.UCSC.mm39.csv

inst/extdata/metadata_phyloP60way.UCSC.mm10.csv

inst/extdata/phyloP100way.UCSC.hg38.chr20.rds

inst/extdata/phyloP100way.UCSC.hg38.chr21.rds

inst/extdata/phyloP100way.UCSC.hg38.chr22.rds

inst/gscores-template/DESCRIPTION

inst/gscores-template/NAMESPACE

inst/gscores-template/R/zzz.R

inst/gscores-template/inst/extdata/.gitkeep

inst/gscores-template/man/package.Rd

inst/scripts/make-data_AlphaMissense.v2023.hg19.R inst/scripts/make-data_AlphaMissense.v2023.hg38.R inst/scripts/make-data_MafDb.1Kgenomes.phase1.GRCh38.R inst/scripts/make-data_MafDb.1Kgenomes.phase1.hs37d5.R inst/scripts/make-data_MafDb.1Kgenomes.phase3.GRCh38.R inst/scripts/make-data_MafDb.1Kgenomes.phase3.hs37d5.R inst/scripts/make-data_MafDb.ExAC.r1.0.GRCh38.R inst/scripts/make-data_MafDb.ExAC.r1.0.hs37d5.R inst/scripts/make-data_MafDb.ExAC.r1.0.nonTCGA.GRCh38.R inst/scripts/make-data_MafDb.ExAC.r1.0.nonTCGA.hs37d5.R inst/scripts/make-data_MafDb.TOPMed.freeze5.hg19.R inst/scripts/make-data_MafDb.TOPMed.freeze5.hg38.R inst/scripts/make-data_MafDb.gnomAD.r2.1.GRCh38.R inst/scripts/make-data_MafDb.gnomAD.r2.1.hs37d5.R inst/scripts/make-data_MafDb.gnomADex.r2.1.GRCh38.R inst/scripts/make-data_MafDb.gnomADex.r2.1.hs37d5.R inst/scripts/make-data_MafH5.gnomAD.v3.1.2.GRCh38.R inst/scripts/make-data_cadd.v1.3.hg19.R inst/scripts/make-data_cadd.v1.6.hg19.R inst/scripts/make-data_cadd.v1.6.hg38.R inst/scripts/make-data_fitCons.UCSC.hg19.R inst/scripts/make-data_linsight.UCSC.hg19.R inst/scripts/make-data_mcap.v1.0.hg19.R inst/scripts/make-data_phastCons100way.UCSC.hg19.R inst/scripts/make-data_phastCons100way.UCSC.hg38.R inst/scripts/make-data_phastCons27way.UCSC.dm6.R inst/scripts/make-data_phastCons30way.UCSC.hg38.R inst/scripts/make-data_phastCons35way.UCSC.mm39.R inst/scripts/make-data_phastCons46wayPlacental.UCSC.hg19.R inst/scripts/make-data_phastCons46wayPrimates.UCSC.hg19.R inst/scripts/make-data_phastCons60way.UCSC.mm10.R inst/scripts/make-data_phastCons7way.UCSC.hg38.R inst/scripts/make-data_phyloP100way.UCSC.hg19.R inst/scripts/make-data_phyloP100way.UCSC.hg38.R inst/scripts/make-data_phyloP35way.UCSC.mm39.R inst/scripts/make-data_phyloP60way.UCSC.mm10.R inst/scripts/make-metadata_AlphaMissense.v2023.hg19.R inst/scripts/make-metadata_AlphaMissense.v2023.hg38.R inst/scripts/make-metadata_MCAP.v1.0.hg19.R inst/scripts/make-metadata_cadd.v1.3.hg19.R inst/scripts/make-metadata_cadd.v1.6.hg19.R inst/scripts/make-metadata_cadd.v1.6.hg38.R inst/scripts/make-metadata_fitCons.UCSC.hg19.R inst/scripts/make-metadata_linsight.UCSC.hg19.R inst/scripts/make-metadata_phastCons100way.UCSC.hg19.R inst/scripts/make-metadata_phastCons100way.UCSC.hg38.R inst/scripts/make-metadata_phastCons27way.UCSC.dm6.R inst/scripts/make-metadata_phastCons30way.UCSC.hg38.R inst/scripts/make-metadata_phastCons35way.UCSC.mm39.R inst/scripts/make-metadata_phastCons46wayPlacental.UCSC.hg19.R inst/scripts/make-metadata_phastCons46wayPrimates.UCSC.hg19.R inst/scripts/make-metadata_phastCons60way.UCSC.mm10.R inst/scripts/make-metadata_phastCons7way.UCSC.hg38.R inst/scripts/make-metadata_phyloP100way.UCSC.hg19.R inst/scripts/make-metadata_phyloP100way.UCSC.hg38.R inst/scripts/make-metadata_phyloP35way.UCSC.mm39.R inst/scripts/make-metadata_phyloP60way.UCSC.mm10.R inst/shinyApp/about.md inst/shinyApp/global.R inst/shinyApp/server.R inst/shinyApp/ui.R

inst/shinyApp/www/GenomicScores.png

inst/shinyApp/www/style.css

inst/unitTests/test_gscores.R inst/unitTests/test_populations.R man/GScores-class.Rd man/GenomicScores-defunct.Rd man/GenomicScores-deprecated.Rd man/availableGScores.Rd man/gscores.Rd man/igscores.Rd man/makeGScoresPackage.Rd man/rgscores.Rd man/wgscores.Rd tests/runTests.R vignettes/GenomicScores.Rmd

vignettes/bibliography.bib

rcastelo/GenomicScores documentation built on April 3, 2024, 10:14 p.m.