Man pages for mil2041/CNCDriver
CNCDriver
| addReplicationTimingSignal | Add replication timing signal value |
| addTriNucleotideDistribution | Add trinucleotide distribution annotations |
| calculatePvalueWithMutCategoryDistributionMatched7 | calculate Pvalue With Mut CategoryDistribution Matched |
| extractElementMutations | Extract overlapping mutations from element annotation bed... |
| get3utrPvalue | Run CNCDriver 3'UTR p-value calculation |
| get3utrPvalueWithPreFilter | Run CNCDriver 3'UTR p-value calculation with mutation... |
| get5utrPvalue | Run CNCDriver 5'UTR p-value calculation |
| get5utrPvalueWithPreFilter | Run CNCDriver 5'UTR p-value calculation with mutation... |
| getCDSPvalue | Run CNCDriver coding region (CDS) p-value calculation |
| getCDSPvalueWithPreFilter | Run CNCDriver coding region (CDS) p-value calculation with... |
| getCDSPvalueWithPreFilter2 | Run CNCDriver coding region (CDS) p-value calculation with... |
| getEnhancerElementPvalue | Run CNCDriver enhancer element p-value calculation |
| getEnhancerElementPvalueWithPreFilter2 | Run CNCDriver enhancer element p-value calculation |
| getEnhancerUnitPvalue | Run CNCDriver enhancer unit p-value calculation |
| getEnhancerUnitPvalueWithPreFilter | Run CNCDriver enhancer unit p-value calculation |
| getEnhancerUnitPvalueWithPreFilter2 | Run CNCDriver enhancer unit p-value calculation |
| getLincRNAPvalue | Run CNCDriver lincRNA p-value calculation |
| getLincRNAPvalueWithPreFilter | Run CNCDriver lincRNA p-value calculation |
| getLincRNAPvalueWithPreFilter2 | Run CNCDriver lincRNA p-value calculation |
| getOpenChromatinElementPvalue | Run CNCDriver open chromatin element p-value calculation |
| getOpenChromatinElementPvalueWithPreFilter2 | Run CNCDriver open chromatin element p-value calculation |
| getPromoterPvalue | Run CNCDriver promoter p-value calculation |
| getPromoterPvalueWithPreFilter | Run CNCDriver promoter p-value calculation with mutation... |
| getPromoterPvalueWithPreFilter2 | Run CNCDriver promoter p-value calculation with mutation... |
| makeElementReplicationTiming | Make replication timing signal value for each regulatory... |
| makeQQplot | make QQ-plot for CNCDriver p-value calculation result |
| mergeVariantPosition | mergeVariantPosition |
| mergeVariantPositionClusterEnhancerUnitV2 | mergeVariantPositionClusterEnhancerUnitV2 |
| mergeVariantPositionClusterV2 | mergeVariantPositionClusterV2 |
| mergeVariantPositionElementClusterV2 | mergeVariantPositionElementClusterV2 |
| mergeVariantPositionSimple | Calculate recurrence number |
| parseMOTIFBR | Parse MOTIFBR annotations from FunSeq2 |
| parseMOTIFG | Parse MOTIFBR annotations from FunSeq2 |
| parseNCENC | Parse NCENC annotations from FunSeq2 |
| parsePosVariantByTriMutContextWithAnnotation5 | Parse Pos Variant By TriMutContext With Annotation |
| parsePosVariantByTriMutContextWithAnnotationCDS | Parse Pos Variant By TriMutContext With Annotation for... |
| reducedFunseqOutputCDS | reduced funseq2 CDS output for LGG |
| reducedFunseqOutputNCDS | reduced funseq2 NCDS output for LGG |
