Man pages for SimonSchafferer/CLIHelperPackage
A packages that manages easy access to cmdLine applications within R (related to RNA-Seq)
| BamToBed_CLI | Constructor method for BamToBed_CLI |
| BamToBed_CLI-class | BamToBed_CLI |
| Bowtie2_CLI | Constructor method for Bowtie2_CLI |
| Bowtie2_CLI-class | Bowtie2_CLI |
| Bowtie2TophatIon_CLI | Constructor method for Bowtie2TophatIon_CLI |
| Bowtie2TophatIon_CLI-class | Bowtie2TophatIon_CLI |
| Bowtie_CLI | Constructor method for Bowtie_CLI |
| Bowtie_CLI-class | Bowtie_CLI |
| CLIApplication-class | CLIApplication Virtual Class |
| CmdGenResult | Constructor method for CmdGenResult |
| CmdGenResult-class | CmdGenResult |
| CmdGenResultExec | Constructor method for CmdGenResultExec |
| CmdGenResultExec-class | CmdGenResultExec |
| Cutadapt_CLI | Constructor method for Cutadapt_CLI |
| Cutadapt_CLI-class | Cutadapt_CLI |
| executeCommandResult | Executes the commands of a executeCommandResult object |
| executeCommandResult-CmdGenResult-method | Executes the commands of a executeCommandResult object |
| FilesOutput | Constructor method for FilesOutput |
| FilesOutput-class | FilesOutput |
| FoldersOutput | Constructor method for FoldersOutput |
| FoldersOutput-class | FoldersOutput |
| generateCommandResult-method | Generates the commands and possibly resulting files/folders |
| Genomecov_CLI | Constructor method for Genomecov_CLI |
| Genomecov_CLI-class | Genomecov_CLI |
| getAddNHTag | Accessor getAddNHTag |
| getAddNHTag-Bowtie_CLI-method | Accessor getAddNHTag |
| getAnnotationFileMB | Accessor annotationFileMB |
| getAnnotationType | Accessor annotationType |
| getBowtieIndexFilePath | Accessor getBowtieIndexFilePath |
| getBowtieIndexFilePath-Bowtie_CLI-method | Accessor getBowtieIndexFilePath |
| getBowtieIndexFilePath-Tophat2_CLI-method | Accessor getBowtieIndexFilePath Tophat2 |
| getCLIApplication | Accessor CLIApplication |
| getCliParams | Accessor getCliParams |
| getCmdGenResult | Accessor getCmdGenResult |
| getCommandLog | Accessor getCommandLog |
| getCommands | Accessor getCommands |
| getExecLog | Accessor getExecLog |
| getExecLogFormatted | Accessor getExecLogFormatted |
| getFilterConditions | Accessor getFilterConditions |
| getFilterSam | Accessor filterSam |
| getGenomeIndexFilePath | Accessor genomeIndexFilePath |
| getGffFile | Accessor HTSeqCount_CLI |
| getGroupVect | Accessor getGroupVect |
| getInFileBam | Accessor getInFileBam |
| getInFileNames | Accessor getInFileNames |
| getInFilePath | Accessor getInFilePath |
| getMatepairFileNames | Accessor getMatepairFileNames |
| getMatepairFileNames-Bowtie_CLI-method | Accessor getMatepairFileNames |
| getOutFileName | Accessor getOutFileName |
| getOutFileName-Genomecov_CLI-method | Accessor getOutFileName |
| getOutFileName-MultiIntersectBed_perl_CLI-method | Accessor getOutFileName |
| getOutFileNames | Accessor getOutFileNames |
| getOutFilePath | Accessor getOutFilePath |
| getOutputFlag | Accessor getOutputFlag |
| getOutputFormat | Accessor getOutputFormat |
| getOutputFormat-BamToBed_CLI-method | Accessor getOutputFormat |
| getOutputFormat-Bowtie_CLI-method | Accessor getOutputFormat |
| getOutputFormat-RNAStar_CLI-method | Accessor getOutputFormat already defined in Samtools |
| getOutputPipeString | Accessor getOutputPipeString |
| getOutResultName | Accessor getOutResultName |
| getOutResultReference | Accessor getOutResultReference |
| getPathToPicardTools | Accessor getPathToPicardTools |
| getPerlPath | Accessor getPerlPath |
| getRequireStrandness | Accessor getRequireStrandness |
| getSamtoolsApplication | Accessor getSamtoolsApplication |
| getSortInFiles | Accessor getSortInFiles |
| getStrandColumn | Accessor getStrandColumn |
| getWithinGroupTH | Accessor getWithinGroupTH |
| HTSeqCount_CLI | Constructor method for HTSeqCount_CLI |
| HTSeqCount_CLI-class | HTSeqCount_CLI |
| IntersectBed_CLI | Constructor method for IntersectBed_CLI |
| IntersectBed_CLI-class | IntersectBed_CLI |
| MergeBedFile_CLI | Constructor method for MergeBedFile_CLI |
| MergeBedFile_CLI-class | MergeBedFile_CLI |
| MultiBamCov_CLI | Constructor method for MultiBamCov_CLI |
| MultiBamCov_CLI-class | MultiBamCov_CLI |
| MultiIntersectBed_CLI | Constructor method for MultiIntersectBed_CLI |
| MultiIntersectBed_CLI-class | MultiIntersectBed_CLI |
| MultiIntersectBed_perl_CLI | Constructor method for MultiIntersectBed_perl_CLI |
| MultiIntersectBed_perl_CLI-class | MultiIntersectBed_perl_CLI |
| OutResultReference | Constructor (factory) for OutResultReference |
| OutResultReference-class | OutResultReference Virtual Class |
| RNAStar_CLI | Constructor method for RNAStar_CLI |
| RNAStar_CLI-class | RNAStar_CLI |
| Samtools_CLI | Constructor method for Samtools_CLI |
| Samtools_CLI-class | Samtools_CLI |
| SortFile_CLI | Constructor method for SortFile_CLI |
| SortFile_CLI-class | SortFile_CLI |
| Tophat2_CLI | Constructor method for Tophat2_CLI |
| Tophat2_CLI-class | Tophat2_CLI |
