Files in SimonSchafferer/CLIHelperPackage
A packages that manages easy access to cmdLine applications within R (related to RNA-Seq)
.Rbuildignore
.gitignore
CLIHelperPackage.Rproj
DESCRIPTION
DESCRIPTION~
LICENSE
NAMESPACE
NAMESPACE~
R/singleRCodeFile.R
README.md
TRUE
additional_notPackaged/CodeForSplittingAndMerging.R
additional_notPackaged/RNAStarCommandsInfos
additional_notPackaged/TemplateForAnalysis.R
additional_notPackaged/TestClasses.R
additional_notPackaged/backupsingleRCodeFile
additional_notPackaged/originalSourceFiles.zip
additional_notPackaged/splitted/BamToBed_CLI.R
additional_notPackaged/splitted/Bowtie2TophatIon_CLI.R
additional_notPackaged/splitted/Bowtie2_CLI.R
additional_notPackaged/splitted/Bowtie_CLI.R
additional_notPackaged/splitted/CLIApplication.R
additional_notPackaged/splitted/CmdGenResult.R
additional_notPackaged/splitted/CmdGenResultExec.R
additional_notPackaged/splitted/Cutadapt_CLI.R
additional_notPackaged/splitted/FilesOutput.R
additional_notPackaged/splitted/FoldersOutput.R
additional_notPackaged/splitted/Genomecov_CLI.R
additional_notPackaged/splitted/HTSeqCount_CLI.R
additional_notPackaged/splitted/IntersectBed_CLI.R
additional_notPackaged/splitted/MergeBedFile_CLI.R
additional_notPackaged/splitted/MultiBamCov_CLI.R
additional_notPackaged/splitted/MultiIntersectBed_CLI.R
additional_notPackaged/splitted/MultiIntersectBed_perl_CLI.R
additional_notPackaged/splitted/OutResultReference.R
additional_notPackaged/splitted/RNAStar_CLI.R
additional_notPackaged/splitted/Samtools_CLI.R
additional_notPackaged/splitted/SortFiles_CLI.R
additional_notPackaged/splitted/Tophat2_CLI.R
data/multiIntersectBed_helper.pl
data/multiIntersectBed_helper.pl~
data/multiIntersectBed_helperBT_2_17.pl
data/multiIntersectBed_helper_deprecated.pl
data/multiIntersectBed_helper_documentation
data/multiIntersectBed_helper_wgth.pl~
man/BamToBed_CLI-class.Rd
man/BamToBed_CLI.Rd
man/Bowtie2TophatIon_CLI-class.Rd
man/Bowtie2TophatIon_CLI.Rd
man/Bowtie2_CLI-class.Rd
man/Bowtie2_CLI.Rd
man/Bowtie_CLI-class.Rd
man/Bowtie_CLI.Rd
man/CLIApplication-class.Rd
man/CmdGenResult-class.Rd
man/CmdGenResult.Rd
man/CmdGenResultExec-class.Rd
man/CmdGenResultExec.Rd
man/Cutadapt_CLI-class.Rd
man/Cutadapt_CLI.Rd
man/FilesOutput-class.Rd
man/FilesOutput.Rd
man/FoldersOutput-class.Rd
man/FoldersOutput.Rd
man/Genomecov_CLI-class.Rd
man/Genomecov_CLI.Rd
man/HTSeqCount_CLI-class.Rd
man/HTSeqCount_CLI.Rd
man/IntersectBed_CLI-class.Rd
man/IntersectBed_CLI.Rd
man/MergeBedFile_CLI-class.Rd
man/MergeBedFile_CLI.Rd
man/MultiBamCov_CLI-class.Rd
man/MultiBamCov_CLI.Rd
man/MultiIntersectBed_CLI-class.Rd
man/MultiIntersectBed_CLI.Rd
man/MultiIntersectBed_perl_CLI-class.Rd
man/MultiIntersectBed_perl_CLI.Rd
man/OutResultReference-class.Rd
man/OutResultReference.Rd
man/RNAStar_CLI-class.Rd
man/RNAStar_CLI.Rd
man/Samtools_CLI-class.Rd
man/Samtools_CLI.Rd
man/SortFile_CLI-class.Rd
man/SortFile_CLI.Rd
man/Tophat2_CLI-class.Rd
man/Tophat2_CLI.Rd
man/executeCommandResult-CmdGenResult-method.Rd
man/executeCommandResult.Rd
man/generateCommandResult-method.Rd
man/getAddNHTag-Bowtie_CLI-method.Rd
man/getAddNHTag.Rd
man/getAnnotationFileMB.Rd
man/getAnnotationType.Rd
man/getBowtieIndexFilePath-Bowtie_CLI-method.Rd
man/getBowtieIndexFilePath-Tophat2_CLI-method.Rd
man/getBowtieIndexFilePath.Rd
man/getCLIApplication.Rd
man/getCliParams.Rd
man/getCmdGenResult.Rd
man/getCommandLog.Rd
man/getCommands.Rd
man/getExecLog.Rd
man/getExecLogFormatted.Rd
man/getFilterConditions.Rd
man/getFilterSam.Rd
man/getGenomeIndexFilePath.Rd
man/getGffFile.Rd
man/getGroupVect.Rd
man/getInFileBam.Rd
man/getInFileNames.Rd
man/getInFilePath.Rd
man/getMatepairFileNames-Bowtie_CLI-method.Rd
man/getMatepairFileNames.Rd
man/getOutFileName-Genomecov_CLI-method.Rd
man/getOutFileName-MultiIntersectBed_perl_CLI-method.Rd
man/getOutFileName.Rd
man/getOutFileNames.Rd
man/getOutFilePath.Rd
man/getOutResultName.Rd
man/getOutResultReference.Rd
man/getOutputFlag.Rd
man/getOutputFormat-BamToBed_CLI-method.Rd
man/getOutputFormat-Bowtie_CLI-method.Rd
man/getOutputFormat-RNAStar_CLI-method.Rd
man/getOutputFormat.Rd
man/getOutputPipeString.Rd
man/getPathToPicardTools.Rd
man/getPerlPath.Rd
man/getRequireStrandness.Rd
man/getSamtoolsApplication.Rd
man/getSortInFiles.Rd
man/getStrandColumn.Rd
man/getWithinGroupTH.Rd
