Files in quevedor2/CCLid
Compares Cancer Cell Line Genotypes Against Pharmacogenomic Datasets
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
Meta/vignette.rds
NAMESPACE
R/assemblePredDat.R
R/assignGrpIds.R
R/bafDrift.R
R/balanceGrps.R
R/cellosaurus_accessors.R
R/checkForConcordance.R
R/compareVcf.R
R/data.R
R/deconvolute_ccl.R
R/demo_data.R
R/downloadRefCCL.R
R/driftOverlap.R
R/formatRefMat.R
R/fullpull.R
R/getCVCL.R
R/globals.R
R/loadRef.R
R/mapVariantFeat.R
R/mapVcf2Affy.R
R/mkPredictions.R
R/overlapPos.R
R/paper_functions.R
R/plot_drift.R
R/segmentDrift.R
R/sigDiffBaf.R
R/similarityMatrix.R
R/splitConcordanceVals.R
R/trainLogit.R
R/utils.R
R/utils_drift.R
R/utils_genotype.R
R/webApp.R
README.md
build/build.R
data-raw/CCLE_CN.gene.RDS
data-raw/DATASET.R
data-raw/GDSC_CN.gene.RDS
data-raw/GNE_CN.gene.RDS
data-raw/GNE_mapping.csv
data-raw/GNE_mapping.tsv
data-raw/GenomeWideSNP_6.hg19.bed.zip
data-raw/GenomeWideSNP_6.na35.annot.filt.csv.gz
data-raw/GenomeWideSNP_6.na35.annot.trimmed.csv.gz
data-raw/HumanOmni2.5-4v1_H.trimmed.csv.gz
data-raw/assembleBafMatrix.R
data-raw/cin70.csv
data-raw/downloadTable.csv
data-raw/pharmacogx_mapping.csv
data-raw/pharmacogx_mapping.xlsx
data-raw/rna_meta_df.csv
data-raw/rna_meta_df.xlsx
data/ccl_table.rda
doc/CCL-vignette.R
doc/CCL-vignette.Rmd
doc/CCL-vignette.html
inst/demo_code/demo_data.R
inst/extdata/A549_trim.vcf.gz
inst/paper_code/benchmark.R
inst/paper_code/drift_it.R
inst/paper_code/drug_it.R
inst/paper_code/logR_pred.R
inst/paper_code/match_it.R
inst/webApp/1_setupid.R
inst/webApp/2_cclid.R
inst/webApp/3_setupdrift.R
inst/webApp/4_drift.R
inst/webApp/5_return.R
man/addSegDat.Rd
man/affy.omni.Rd
man/annoDemoMat.Rd
man/annotateSegments.Rd
man/assemblePredDat.Rd
man/assignGrpIDs.Rd
man/availableRefCCL.Rd
man/bafDrift.Rd
man/balanceGrps.Rd
man/ccl_table.Rd
man/checkAgainst.Rd
man/checkForConcordance.Rd
man/checkMse.Rd
man/cin70.Rd
man/combineSamples.Rd
man/compareVcf.Rd
man/corWithDrug.Rd
man/demoSample.Rd
man/dot-addCumPos.Rd
man/dot-addSegSd.Rd
man/dot-blankGr.Rd
man/dot-chkAndDownload.Rd
man/dot-compSegs.Rd
man/dot-demo.Rd
man/dot-demoDeconvolution.Rd
man/dot-estimateDrift.Rd
man/dot-estimateZcutoff.Rd
man/dot-filt.Rd
man/dot-fixGT.Rd
man/dot-genMatchSnpDiff.Rd
man/dot-genNonmatchSnpDiff.Rd
man/dot-getChrLength.Rd
man/dot-getDerivedFrom.Rd
man/dot-getDrift.Rd
man/dot-getSynonymous.Rd
man/dot-getVariantFeatures.Rd
man/dot-grepNA.Rd
man/dot-jsonToGr.Rd
man/dot-meltDf.Rd
man/dot-normBAF.Rd
man/dot-overlapProbeset.Rd
man/dot-revComp.Rd
man/dot-vcf2AffyGT.Rd
man/dot-zval.Rd
man/downloadRefCCL.Rd
man/driftOverlap.Rd
man/driftOverlapMetric.Rd
man/findCclPairs.Rd
man/formatRefMat.Rd
man/fullpull.Rd
man/genDemoData.Rd
man/genErrBp.Rd
man/getBafDrifts.Rd
man/getCNDrifts.Rd
man/getCVCL.Rd
man/getCinScore.Rd
man/getGeneExpr.Rd
man/getGenes.Rd
man/getSegSD.Rd
man/getVcfDrifts.Rd
man/gne.meta.Rd
man/loadInPSets.Rd
man/loadRef.Rd
man/mapVariantFeat.Rd
man/mapVcf2Affy.Rd
man/meta.df.Rd
man/mkPredictions.Rd
man/multiDriftPlot.Rd
man/overlapPos.Rd
man/plot.CCLid.Rd
man/plot.SimpleCCLid.Rd
man/plot.multiObj.Rd
man/plotFracDrift.Rd
man/plotHist.Rd
man/readinRnaFileMapping.Rd
man/rna.meta.df.Rd
man/segmentDrift.Rd
man/sigDiffBaf.Rd
man/similarityMatrix.Rd
man/snp6.dat.Rd
man/splitConcordanceVals.Rd
man/splitToMNM.Rd
man/summarizeFracDrift.Rd
man/trainLogit.Rd
vignettes/.gitignore
vignettes/CCL-vignette.Rmd
