Man pages for tgirke/systemPipeR
systemPipeR: Workflow Environment for Data Analysis and Report Generation
| add-methods | Extension accessor methods for SummarizedExperiment object |
| alignStats | Alignment statistics |
| catDB-class | Class '"catDB"' |
| catmap | catDB accessor methods |
| check.output | Checking if the outfiles files exist |
| clusterRun | Submit command-line tools to cluster |
| config.param | Adding param file |
| configWF | Workflow Steps Selection |
| countRangeset | Read counting for several range sets |
| createParamFiles | createParam |
| cwlFilesUpdate | Update CWL description 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 |
| GOHyperGAll | GO term enrichment analysis for large numbers of gene sets |
| importWF | Import R Markdown file as workflow |
| INTERSECTset-class | Class '"INTERSECTset"' |
| LineWise-class | Class '"LineWise"' |
| listCmdTools | List/check the existence of command-line tools of a workflow |
| loadWorkflow | Constructs SYSargs2 object from CWL param and targets files |
| mergeBamByFactor | Merge BAM files based on factor |
| moduleload | Interface to allow full use of the Environment Modules 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 |
| ParamFiles | Accessories function to modify the Command-line Version 1 |
| ParamFiles2 | Accessories function to modify the Command-line Version 2 |
| plotfeatureCoverage | Plot feature coverage results |
| plotfeaturetypeCounts | Plot read distribution across genomic features |
| plotWF | Visualize SPR workflow and status |
| predORF | Predict ORFs |
| preprocessReads | Run custom read preprocessing functions |
| readComp | Import sample comparisons from targets file |
| renderLogs | Render RMarkdown Logs Report |
| renderReport | Render RMarkdown Report |
| returnRPKM | RPKM Normalization |
| runCommandline | Execute SYSargs and SYSargs2 |
| run_DESeq2 | Runs DESeq2 |
| runDiff | Differential abundance analysis for many range sets |
| run_edgeR | Runs edgeR |
| runWF | Execute SYSargsList |
| sal2bash | Translate SYSargsList back to a bash workflow |
| sal2rmd | Translate SYSargsList back to a workflow template Rmarkdown... |
| scaleRanges | Scale spliced ranges to genome coordinates |
| seeFastq | Quality reports for FASTQ files |
| showDF | Create an HTML table using DT package with fixed columns |
| SPRproject | Workflow Project Initiation |
| subsetWF | Subsetting SYSargs2 class slots |
| symLink2bam | Symbolic links for IGV |
| sysargs | SYSargs accessor methods |
| SYSargs2-class | Class '"SYSargs2"' |
| SYSargs-class | Class '"SYSargs"' |
| SYSargsList | SYSargsList Constructor |
| SYSargsList-class | Class '"SYSargsList"' |
| systemArgs | Constructs SYSargs object from param and targets files |
| systemPipeR-package | systemPipeR package for Workflow Environment |
| targets.as.df | Convert targets to list or data.frame |
| trimbatch | Genome read coverage by transcript models |
| tryCMD | 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"' |
| write_SYSargsList | Writeout SYSargsList object |
| writeTargets | Write updated targets out to file from 'SYSargsList' |
| writeTargetsout | Write updated targets out to file |
| writeTargetsRef | Generate targets file with reference |
