Man pages for systemPipeR
systemPipeR: NGS workflow and report generation environment
| alignStats | Alignment statistics |
| catDB-class | Class '"catDB"' |
| catmap | catDB accessor methods |
| clusterRun | Submit command-line tools to cluster |
| config.param | Adding param file |
| configWF | Workflow Steps Selection |
| countRangeset | Read counting for several range sets |
| createWF | Constructs SYSargs2 object and creates CWL param files |
| EnvModules-class | Class '"EnvModules"' |
| evalCode | Toggles option 'eval' on the RMarkdown files |
| 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 |
| GOHyperGAll | GO term enrichment analysis for large numbers of gene sets |
| initWF | Workflow Project Initiation |
| INTERSECTset-class | Class '"INTERSECTset"' |
| loadWorkflow | Constructs SYSargs2 object from CWL param and targets files |
| mergeBamByFactor | Merge BAM files based on factor |
| module | Interface to allow full use of the Environment Modules system... |
| moduleload | Interface to module system |
| olBarplot | Bar plot for intersect sets |
| olRanges | Identify Range Overlaps for IRanges and GRanges Object |
| output_update | Updates the output files paths in the 'SYSargs2' object |
| overLapper | Set Intersect and Venn Diagram Functions |
| plotfeatureCoverage | Plot feature coverage results |
| plotfeaturetypeCounts | Plot read distribution across genomic features |
| plotWF | Graphviz Plot Workflow |
| predORF | Predict ORFs |
| preprocessReads | Run custom read preprocessing functions |
| qsubRun | Submit command-line tools to cluster |
| readComp | Import sample comparisons from targets file |
| renderReport | Render RMarkdown Report |
| renderWF | Populate all the command-line in an 'SYSargs2' object |
| returnRPKM | RPKM Normalization |
| runCommandline | Execute SYSargs and SYSargs2 |
| run_DESeq2 | Runs DESeq2 |
| runDiff | Differential abundance analysis for many range sets |
| run_edgeR | Runs edgeR |
| run_track | Deprecated 'run_track' functions |
| runWF | Execute SYSargsList |
| scaleRanges | Scale spliced ranges to genome coordinates |
| seeFastq | Quality reports for FASTQ files |
| subsetWF | Subsetting SYSargs2 class slots |
| symLink2bam | Symbolic links for IGV |
| sysargs | SYSargs accessor methods |
| SYSargs2-class | Class '"SYSargs2"' |
| sysargs2-methods | SYSargs2 accessor methods |
| SYSargs2Pipe-class | Deprecated '"SYSargs2Pipe"' Class |
| SYSargs2Pipe-methods | Deprecated '"SYSargs2Pipe"' accessor methods |
| SYSargs-class | Class '"SYSargs"' |
| SYSargsList-class | Class '"SYSargsList"' |
| sysargslist-methods | SYSargsList accessor methods |
| systemArgs | Constructs SYSargs object from param and targets files |
| targets.as.df | Convert targets list to data.frame |
| tryCL | Collect information about the third-party software |
| tryPath | Validation of the files or directories |
| variantReport | Generate Variant Report |
| vennPlot | Plot 2-5 way Venn diagrams |
| VENNset-class | Class '"VENNset"' |
| writeTargetsout | Write updated targets out to file |
| writeTargetsRef | Generate targets file with reference |
