EnvModules-class        Class '"EnvModules"'
GOHyperGAll             GO term enrichment analysis for large numbers
                        of gene sets
INTERSECTset-class      Class '"INTERSECTset"'
LineWise-class          Class '"LineWise"'
SPRproject              Workflow Project Initiation
SYSargs-class           Class '"SYSargs"'
SYSargs2-class          Class '"SYSargs2"'
SYSargsList             SYSargsList Constructor
SYSargsList-class       Class '"SYSargsList"'
VENNset-class           Class '"VENNset"'
addAssay-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
createParam             createParam
cwlFilesUpdate          Update CWL description files
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
importWF                Import R Markdown file as 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 for Unix
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
plotWF                  Visualize SPR workflow and status
plotfeatureCoverage     Plot feature coverage results
plotfeaturetypeCounts   Plot read distribution across genomic features
predORF                 Predict ORFs
preprocessReads         Run custom read preprocessing functions
printParam              Accessories function to modify the Command-line
                        Version 1
printParam2             Accessories function to modify the Command-line
                        Version 2
readComp                Import sample comparisons from targets file
renderLogs              Render RMarkdown Logs Report
renderReport            Render RMarkdown Report
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
sal2bash                Translate SYSargsList back to a bash workflow
sal2rmd                 Translate SYSargsList back to a workflow
                        template Rmarkdown file
scaleRanges             Scale spliced ranges to genome coordinates
seeFastq                Quality reports for FASTQ files
showDF                  Create an HTML table using DT package with
                        fixed columns
subsetWF                Subsetting SYSargs2 class slots
symLink2bam             Symbolic links for IGV
sysargs                 SYSargs accessor methods
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
writeTargets            Write updated targets out to file from
                        'SYSargsList'
writeTargetsRef         Generate targets file with reference
writeTargetsout         Write updated targets out to file
write_SYSargsList       Writeout SYSargsList object
