A C F G I L M N O P Q R S T V W misc
| alignStats | Alignment statistics |
| as.list-method | Class '"INTERSECTset"' |
| as.list-method | Class '"VENNset"' |
| catDB-class | Class '"catDB"' |
| catlist | catDB accessor methods |
| catlist-method | Class '"catDB"' |
| catlist-methods | catDB accessor methods |
| catmap | catDB accessor methods |
| catmap-method | Class '"catDB"' |
| catmap-methods | catDB accessor methods |
| clusterRun | Submit command-line tools to cluster |
| coerce-method | Class '"INTERSECTset"' |
| coerce-method | Class '"SYSargs"' |
| coerce-method | Class '"VENNset"' |
| coerce-method | Class '"catDB"' |
| combineVarReports | Generate Variant Report |
| complexitylevels | Set Intersect and Venn Diagram Functions |
| complexitylevels-method | Class '"INTERSECTset"' |
| complexitylevels-method | Class '"VENNset"' |
| complexitylevels-methods | Set Intersect and Venn Diagram Functions |
| cores | SYSargs accessor methods |
| cores-method | Class '"SYSargs"' |
| cores-methods | SYSargs accessor methods |
| countRangeset | Read counting for several range sets |
| featureCoverage | Genome read coverage by transcript models |
| featuretypeCounts | Plot read distribution across genomic features |
| filterDEGs | Filter and plot DEG results |
| filterVars | Filter VCF files |
| genFeatures | Generate feature ranges from TxDb |
| getQsubargs | Arguments for qsub |
| goBarplot | GO term enrichment analysis for large numbers of gene sets |
| GOCluster_Report | GO term enrichment analysis for large numbers of gene sets |
| GOHyperGAll | GO term enrichment analysis for large numbers of gene sets |
| GOHyperGAll_Simplify | GO term enrichment analysis for large numbers of gene sets |
| GOHyperGAll_Subset | GO term enrichment analysis for large numbers of gene sets |
| idconv | catDB accessor methods |
| idconv-method | Class '"catDB"' |
| idconv-methods | catDB accessor methods |
| infile1 | SYSargs accessor methods |
| infile1-method | Class '"SYSargs"' |
| infile1-methods | SYSargs accessor methods |
| infile2 | SYSargs accessor methods |
| infile2-method | Class '"SYSargs"' |
| infile2-methods | SYSargs accessor methods |
| intersectlist | Set Intersect and Venn Diagram Functions |
| intersectlist-method | Class '"INTERSECTset"' |
| intersectlist-methods | Set Intersect and Venn Diagram Functions |
| intersectmatrix | Set Intersect and Venn Diagram Functions |
| intersectmatrix-method | Class '"INTERSECTset"' |
| intersectmatrix-method | Class '"VENNset"' |
| intersectmatrix-methods | Set Intersect and Venn Diagram Functions |
| INTERSECTset-class | Class '"INTERSECTset"' |
| length-method | Class '"INTERSECTset"' |
| length-method | Class '"SYSargs"' |
| length-method | Class '"VENNset"' |
| makeCATdb | GO term enrichment analysis for large numbers of gene sets |
| mergeBamByFactor | Merge BAM files based on factor |
| modulelist | Interface to module system |
| moduleload | Interface to module system |
| modules | SYSargs accessor methods |
| modules-method | Class '"SYSargs"' |
| modules-methods | SYSargs accessor methods |
| names-method | Class '"INTERSECTset"' |
| names-method | Class '"SYSargs"' |
| names-method | Class '"VENNset"' |
| names-method | Class '"catDB"' |
| olBarplot | Bar plot for intersect sets |
| other | SYSargs accessor methods |
| other-method | Class '"SYSargs"' |
| other-methods | SYSargs accessor methods |
| outfile1 | SYSargs accessor methods |
| outfile1-method | Class '"SYSargs"' |
| outfile1-methods | SYSargs accessor methods |
| outpaths | SYSargs accessor methods |
| outpaths-method | Class '"SYSargs"' |
| outpaths-methods | SYSargs accessor methods |
| overLapper | Set Intersect and Venn Diagram Functions |
| plotfeatureCoverage | Plot feature coverage results |
| plotfeaturetypeCounts | Plot read distribution across genomic features |
| predORF | Predict ORFs |
| preprocessReads | Run custom read preprocessing functions |
| qsubRun | Submit command-line tools to cluster |
| readComp | Import sample comparisons from targets file |
| reference | SYSargs accessor methods |
| reference-method | Class '"SYSargs"' |
| reference-methods | SYSargs accessor methods |
| results | SYSargs accessor methods |
| results-method | Class '"SYSargs"' |
| results-methods | SYSargs accessor methods |
| returnRPKM | RPKM Normalization |
| runCommandline | Execute SYSargs |
| runDiff | Differential abundance analysis for many range sets |
| run_DESeq2 | Runs DESeq2 |
| run_edgeR | Runs edgeR |
| SampleName | SYSargs accessor methods |
| SampleName-method | Class '"SYSargs"' |
| SampleName-methods | SYSargs accessor methods |
| scaleRanges | Scale spliced ranges to genome coordinates |
| seeFastq | Quality reports for FASTQ files |
| seeFastqPlot | Quality reports for FASTQ files |
| setlist | Set Intersect and Venn Diagram Functions |
| setlist-method | Class '"INTERSECTset"' |
| setlist-method | Class '"VENNset"' |
| setlist-methods | Set Intersect and Venn Diagram Functions |
| show-method | Class '"INTERSECTset"' |
| show-method | Class '"SYSargs"' |
| show-method | Class '"VENNset"' |
| show-method | Class '"catDB"' |
| software | SYSargs accessor methods |
| software-method | Class '"SYSargs"' |
| software-methods | SYSargs accessor methods |
| symLink2bam | Symbolic links for IGV |
| sysargs | SYSargs accessor methods |
| SYSargs-class | Class '"SYSargs"' |
| sysargs-method | Class '"SYSargs"' |
| sysargs-methods | SYSargs accessor methods |
| systemArgs | Constructs SYSargs object from param and targets files |
| targetsheader | SYSargs accessor methods |
| targetsheader-method | Class '"SYSargs"' |
| targetsheader-methods | SYSargs accessor methods |
| targetsin | SYSargs accessor methods |
| targetsin-method | Class '"SYSargs"' |
| targetsin-methods | SYSargs accessor methods |
| targetsout | SYSargs accessor methods |
| targetsout-method | Class '"SYSargs"' |
| targetsout-methods | SYSargs accessor methods |
| variantReport | Generate Variant Report |
| varSummary | Generate Variant Report |
| vennlist | Set Intersect and Venn Diagram Functions |
| vennlist-method | Class '"VENNset"' |
| vennlist-methods | Set Intersect and Venn Diagram Functions |
| vennPlot | Plot 2-5 way Venn diagrams |
| VENNset-class | Class '"VENNset"' |
| writeTargetsout | Write updated targets out to file |
| writeTargetsRef | Generate targets file with reference |
| [-method | Class '"SYSargs"' |