Man pages for RGLab/RNASeqPipelineR
Construct Standardized pipelines for processing RNASeq data

AlignmentSTARUse the STAR tool to align the reads
annotateSRAAnnotate the SRA file pData
annotateUCSCAnnotate features: map UCSC gene cluster id to gene symbols
annotationsFromSRXQuick and dirty annotations from SRAmetadb
assignConfigAssign a new element to the RNASeqPipelineR configuration
buildGenomeIndexSTARBuild a genome index for STAR
buildGenomeIndexSTAR2Build a reference genome 2
buildReferenceBuild a reference genome
concatenateFastqConcatenate FastQ files
configure_projectConfigure the project and store info in namespace
convertSRAtoFastQConvert SRA files to FastQ
createProjectCreate a new RNASeqPipeline project
detectAsperaDetect and configure the aspera client location
devel_truncateDataUtility function to truncate the test data to 'n' SRA files...
downloadSRADownload FastQ files based on Immport data and SRA db, unless...
getAndConnectSRAdbChecks if the SRAdb sqlite database is available
getConfigGet the configuration for the project from the namespace
getConfigDirRetrieve full path to 'dir' in project configuration...
getConfigFileRetrieve full path to 'dir/file' in project configuration...
getDataFromSRXDownload SRA files from SRX accessions
getDirObtain directory path for configuration variable.
getExpressionSetReturn and expression set of the counts or TPM values
kallistoAlignUse the Kallisto tool to align and quantify RNASeq FASTQ...
kallistoAssembleOutputAssemble kallisto output into a single table.
kallistoAssembleQCCollect kallisto and fastqc information.
kallistoBuildTranscriptIndexkallisto methods
kallistoReadQCAssemble kallisto quality control information
loadImmportTablesLoad data from Immport tables
loadProjectLoad an RNASeqPipelineR project
mergeDataMap the annotation file to the count and tpm data
MiTCRRun MiTCR on each fastQ file
pearRun PEAR to assemble paired-end fastq files into one files.
pipelineReportProduce a report listing the tools and packages used by the...
QualityControlGenerate QualityControl Matric.
qualityRNASeQCRun RNASeQC quality control
readConfigRead the configuration for a project
RNASeqPipelineSimplify pipelining RNASeq data
RSEMAssembleExpressionMatrixAssemble an expression matrix of all results
RSEMCalculateExpressionUse the RSEM tool to annotate and quantify the reads
RSEMSummarizeMappingSummarize the number of mapped, unmapped and ambiguous reads...
runFastQCPerform FastQC quality control
saveConfigSave the configuration for a project
sequenceAlignmentTopHatUse the Tophat tool to align reads
setGenomeReferenceSet path to reference genome index
SRAOverviewOverview of downloaded files
sumDuplicatesSum all read counts for multiple instances of a single gene...
summarizeDuplicationSummarize duplication statistics from fastqc
summarizeFastQCSummarize the fastQC results
RGLab/RNASeqPipelineR documentation built on June 24, 2018, 6:34 p.m.