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A C D E F G I L M N O P Q R S T V W Y misc
| alignStats | Alignment statistics |
| as.list-method | Class '"INTERSECTset"' |
| as.list-method | Class '"VENNset"' |
| available_modules-method | Class '"EnvModules"' |
| 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 |
| clt | SYSargs2 accessor methods |
| clt-method | Class '"SYSargs2"' |
| clt-methods | SYSargs2 accessor methods |
| clusterRun | Submit command-line tools to cluster |
| cmdlist | SYSargs2 accessor methods |
| cmdlist-method | Class '"SYSargs2"' |
| cmdlist-methods | SYSargs2 accessor methods |
| codeSteps | SYSargsList accessor methods |
| codeSteps-method | Class '"SYSargsList"' |
| codeSteps-methods | SYSargsList accessor methods |
| coerce-method | Class '"EnvModules"' |
| coerce-method | Class '"INTERSECTset"' |
| coerce-method | Class '"SYSargs"' |
| coerce-method | Class '"SYSargs2"' |
| coerce-method | Deprecated '"SYSargs2Pipe"' Class |
| coerce-method | Class '"SYSargsList"' |
| 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 |
| config.param | Adding param file |
| configWF | Workflow Steps Selection |
| cores | SYSargs accessor methods |
| cores-method | Class '"SYSargs"' |
| cores-methods | SYSargs accessor methods |
| countRangeset | Read counting for several range sets |
| createWF | Constructs SYSargs2 object and creates CWL param files |
| cwlfiles | SYSargs2 accessor methods |
| cwlfiles-method | Class '"SYSargs2"' |
| cwlfiles-methods | SYSargs2 accessor methods |
| dataWF | SYSargsList accessor methods |
| dataWF-method | Class '"SYSargsList"' |
| dataWF-methods | SYSargsList accessor methods |
| default_modules-method | Class '"EnvModules"' |
| EnvModules-class | Class '"EnvModules"' |
| EnvModules-method | 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 |
| 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-method | Class '"SYSargs2"' |
| infile1-methods | SYSargs accessor methods |
| infile2 | SYSargs accessor methods |
| infile2-method | Class '"SYSargs"' |
| infile2-method | Class '"SYSargs2"' |
| infile2-methods | SYSargs accessor methods |
| initProject | Workflow Project Initiation |
| initWF | Workflow Project Initiation |
| input | SYSargs2 accessor methods |
| input-method | Class '"SYSargs2"' |
| input-methods | SYSargs2 accessor methods |
| inputvars | SYSargs2 accessor methods |
| inputvars-method | Class '"SYSargs2"' |
| inputvars-methods | SYSargs2 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 '"SYSargs2"' |
| length-method | Deprecated '"SYSargs2Pipe"' Class |
| length-method | Class '"SYSargsList"' |
| length-method | Class '"VENNset"' |
| loaded_modules-method | Class '"EnvModules"' |
| loadWF | Constructs SYSargs2 object from CWL param and targets files |
| loadWorkflow | Constructs SYSargs2 object from CWL param and targets files |
| makeCATdb | GO term enrichment analysis for large numbers of gene sets |
| mergeBamByFactor | Merge BAM files based on factor |
| module | Interface to allow full use of the Environment Modules system for Unix |
| moduleAvail | Interface to module system |
| moduleClear | Interface to module system |
| modulecmd-method | Class '"EnvModules"' |
| moduleInit | Interface to module system |
| modulelist | Interface to module system |
| moduleload | Interface to module system |
| modules | SYSargs accessor methods |
| modules-method | Class '"SYSargs"' |
| modules-method | Class '"SYSargs2"' |
| modules-methods | SYSargs accessor methods |
| moduleUnload | Interface to module system |
| names-method | Class '"EnvModules"' |
| names-method | Class '"INTERSECTset"' |
| names-method | Class '"SYSargs"' |
| names-method | Class '"SYSargs2"' |
| names-method | Deprecated '"SYSargs2Pipe"' Class |
| names-method | Class '"SYSargsList"' |
| names-method | Class '"VENNset"' |
| names-method | Class '"catDB"' |
| olBarplot | Bar plot for intersect sets |
| olRanges | Identify Range Overlaps for IRanges and GRanges Object |
| 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 |
| output | SYSargs2 accessor methods |
| output-method | Class '"SYSargs2"' |
| output-methods | SYSargs2 accessor methods |
| 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 |
| projectWF | SYSargsList accessor methods |
| projectWF-method | Class '"SYSargsList"' |
| projectWF-methods | SYSargsList accessor methods |
| 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 |
| renderReport | Render RMarkdown Report |
| renderWF | Populate all the command-line in an 'SYSargs2' object |
| results | SYSargs accessor methods |
| results-method | Class '"SYSargs"' |
| results-methods | SYSargs accessor methods |
| returnRPKM | RPKM Normalization |
| runCommandline | Execute SYSargs and SYSargs2 |
| runDiff | Differential abundance analysis for many range sets |
| runWF | Execute SYSargsList |
| run_DESeq2 | Runs DESeq2 |
| run_edgeR | Runs edgeR |
| run_track | Deprecated 'run_track' functions |
| 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 '"EnvModules"' |
| show-method | Class '"INTERSECTset"' |
| show-method | Class '"SYSargs"' |
| show-method | Class '"SYSargs2"' |
| show-method | Deprecated '"SYSargs2Pipe"' Class |
| show-method | Class '"SYSargsList"' |
| show-method | Class '"VENNset"' |
| show-method | Class '"catDB"' |
| software | SYSargs accessor methods |
| software-method | Class '"SYSargs"' |
| software-methods | SYSargs accessor methods |
| statusWF | SYSargsList accessor methods |
| statusWF-method | Class '"SYSargsList"' |
| statusWF-methods | SYSargsList accessor methods |
| stepsWF | SYSargsList accessor methods |
| stepsWF-method | Class '"SYSargsList"' |
| stepsWF-methods | SYSargsList accessor methods |
| subsetWF | Subsetting SYSargs2 class slots |
| summaryWF | Deprecated '"SYSargs2Pipe"' accessor methods |
| summaryWF-method | Deprecated '"SYSargs2Pipe"' Class |
| summaryWF-method | Class '"SYSargsList"' |
| summaryWF-methods | Deprecated '"SYSargs2Pipe"' accessor methods |
| symLink2bam | Symbolic links for IGV |
| sysargs | SYSargs accessor methods |
| SYSargs-class | Class '"SYSargs"' |
| sysargs-method | Class '"SYSargs"' |
| sysargs-methods | SYSargs accessor methods |
| sysargs2 | SYSargs2 accessor methods |
| SYSargs2-class | Class '"SYSargs2"' |
| sysargs2-method | Class '"SYSargs2"' |
| sysargs2-method | SYSargs2 accessor methods |
| SYSargs2Pipe-class | Deprecated '"SYSargs2Pipe"' Class |
| SYSargs2Pipe-method | Deprecated '"SYSargs2Pipe"' accessor methods |
| SYSargs2Pipe_ls | Deprecated '"SYSargs2Pipe"' accessor methods |
| SYSargs2Pipe_ls-method | Deprecated '"SYSargs2Pipe"' Class |
| SYSargs2_steps | SYSargsList accessor methods |
| SYSargs2_steps-method | Class '"SYSargsList"' |
| SYSargs2_steps-methods | SYSargsList accessor methods |
| sysargslist | SYSargsList accessor methods |
| SYSargsList-class | Class '"SYSargsList"' |
| sysargslist-method | Class '"SYSargsList"' |
| sysargslist-method | SYSargsList accessor methods |
| sysconfig | SYSargsList accessor methods |
| sysconfig-method | Class '"SYSargsList"' |
| sysconfig-methods | SYSargsList accessor methods |
| SYSproject | Workflow Project Initiation |
| systemArgs | Constructs SYSargs object from param and targets files |
| targets | SYSargs2 accessor methods |
| targets-method | Class '"SYSargs2"' |
| targets-methods | SYSargs2 accessor methods |
| targets.as.df | Convert targets list to data.frame |
| targetsheader | SYSargs accessor methods |
| targetsheader-method | Class '"SYSargs"' |
| targetsheader-method | Class '"SYSargs2"' |
| 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 |
| track | Deprecated '"SYSargs2Pipe"' accessor methods |
| track-method | Deprecated '"SYSargs2Pipe"' Class |
| track-methods | Deprecated '"SYSargs2Pipe"' accessor methods |
| tryCL | Collect information about the third-party software |
| tryPath | Validation of the files or directories |
| 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"' |
| wf | SYSargs2 accessor methods |
| wf-method | Class '"SYSargs2"' |
| wf-methods | SYSargs2 accessor methods |
| WF_steps | Deprecated '"SYSargs2Pipe"' accessor methods |
| WF_steps-method | Deprecated '"SYSargs2Pipe"' Class |
| WF_steps-methods | Deprecated '"SYSargs2Pipe"' accessor methods |
| writeTargetsout | Write updated targets out to file |
| writeTargetsRef | Generate targets file with reference |
| yamlinput | SYSargs2 accessor methods |
| yamlinput-method | Class '"SYSargs2"' |
| yamlinput-methods | SYSargs2 accessor methods |
| $-method | Class '"EnvModules"' |
| $-method | Class '"SYSargs2"' |
| $-method | Deprecated '"SYSargs2Pipe"' Class |
| $-method | Class '"SYSargsList"' |
| [-method | Class '"EnvModules"' |
| [-method | Class '"SYSargs"' |
| [-method | Class '"SYSargs2"' |
| [-method | Deprecated '"SYSargs2Pipe"' Class |
| [-method | Class '"SYSargsList"' |
| [[-method | Class '"EnvModules"' |
| [[-method | Class '"SYSargs2"' |
| [[-method | Deprecated '"SYSargs2Pipe"' Class |
| [[-method | Class '"SYSargsList"' |
| [[<--method | Class '"EnvModules"' |
| [[<--method | Class '"SYSargs2"' |
| [[<--method | Deprecated '"SYSargs2Pipe"' Class |
| [[<--method | Class '"SYSargsList"' |