Files in mil2041/CNCDriver

CNCDriver

.Rbuildignore

.gitignore

.travis.yml

CNCDriver.Rproj

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/data.R R/get3utrPvalue.R R/get3utrPvalue_cluster.R R/get5utrPvalue.R R/get5utrPvalue_cluster.R R/getCDSPvalue.R R/getCDSPvalue_cluster_v1.R R/getCDSPvalue_cluster_v2.R R/getEnhancerElementPvalue.R R/getEnhancerElementPvalue_cluster_v2.R R/getEnhancerUnitPvalue.R R/getEnhancerUnitPvalue_cluster.R R/getEnhancerUnitPvalue_cluster_v2.R R/getLincRNAPvalue.R R/getLincRNAPvalue_cluster.R R/getLincRNAPvalue_cluster_v2.R R/getOpenChromatinElementPvalue.R R/getOpenChromatinElementPvalue_cluster_v2.R R/getPromoterPvalue.R R/getPromoterPvalue_cluster.R R/getPromoterPvalue_cluster_v2.R R/makeQQplot.R R/replicationTiming-addReplicationTimingsignal.R R/replicationTiming-makeElementReplicationTiming.R R/somaticSignature-addTriNucleotideDistribution.R R/utils-calculatePvalueWithMutCategoryDistributionMatched7.R R/utils-extractElementMutations.R R/utils-makeQQplot.R R/utils-mergeVariantPositionSimple.R R/utils-mergeVariantPosition_v7.R R/utils-mergeVariantPosition_v7_Element_Cluster.R R/utils-mergeVariantPosition_v7_cluster_v2.R R/utils-mergeVariantPosition_v7_enhancerUnit_Cluster.R

R/utils-parseFunseq2Annotation.R

R/utils-parseMOTIFBR.R R/utils-parseMOTIFG.R R/utils-parseNCENC.R R/utils-parsePosVariantByTriMutcontextWithAnnotation5.R R/utils-parsePosVariantByTriMutcontextWithAnnotationCDS.R README.md

_config.yml

cnc_driver_docker/.gitattributes

cnc_driver_docker/README.md

cnc_driver_docker/cnc_driver_docker.tar.gz

cnc_driver_docker/run_docker_cncdriver.sh

cnc_driver_docker/sample_cncdriver.R

data/reducedFunseqOutputCDS.rda

data/reducedFunseqOutputNCDS.rda

man/addReplicationTimingSignal.Rd man/addTriNucleotideDistribution.Rd man/calculatePvalueWithMutCategoryDistributionMatched7.Rd man/extractElementMutations.Rd man/get3utrPvalue.Rd man/get3utrPvalueWithPreFilter.Rd man/get5utrPvalue.Rd man/get5utrPvalueWithPreFilter.Rd man/getCDSPvalue.Rd man/getCDSPvalueWithPreFilter.Rd man/getCDSPvalueWithPreFilter2.Rd man/getEnhancerElementPvalue.Rd man/getEnhancerElementPvalueWithPreFilter2.Rd man/getEnhancerUnitPvalue.Rd man/getEnhancerUnitPvalueWithPreFilter.Rd man/getEnhancerUnitPvalueWithPreFilter2.Rd man/getLincRNAPvalue.Rd man/getLincRNAPvalueWithPreFilter.Rd man/getLincRNAPvalueWithPreFilter2.Rd man/getOpenChromatinElementPvalue.Rd man/getOpenChromatinElementPvalueWithPreFilter2.Rd man/getPromoterPvalue.Rd man/getPromoterPvalueWithPreFilter.Rd man/getPromoterPvalueWithPreFilter2.Rd man/makeElementReplicationTiming.Rd man/makeQQplot.Rd man/mergeVariantPosition.Rd man/mergeVariantPositionClusterEnhancerUnitV2.Rd man/mergeVariantPositionClusterV2.Rd man/mergeVariantPositionElementClusterV2.Rd man/mergeVariantPositionSimple.Rd man/parseMOTIFBR.Rd man/parseMOTIFG.Rd man/parseNCENC.Rd man/parsePosVariantByTriMutContextWithAnnotation5.Rd man/parsePosVariantByTriMutContextWithAnnotationCDS.Rd man/reducedFunseqOutputCDS.Rd man/reducedFunseqOutputNCDS.Rd tmp/datasetDocument.R tmp/getCDSPvalue_cluster_v1.R tmp/makeQQplot.R tmp/makeQQplot_v2.R tmp/tutorial.R tmp/tutorial_July_2020.R tmp/tutorial_mac_PCAWG_annotation.R tmp/tutorial_test_v5.R tmp/tutorial_test_v8_1.R tmp/tutorial_v3.R tmp/tutorial_v7.R tmp/tutorial_v8.R tmp/utils-mergeVariantPositionSimple.R tmp/utils-mergeVariantPosition_v7_cluster_v2.R

tmp/utils-parseFunseq2Annotation.R

tmp/utils-preProcessVCF.R vignettes/cncdriverTutorial.Rmd

vignettes/cncdriverTutorial.html

vignettes/cncdriverTutorial.nb.html

mil2041/CNCDriver documentation built on Dec. 13, 2020, 3:41 a.m.