All functions

EnvModules-class [[,EnvModules,ANY,missing-method [[ [,EnvModules,ANY,ANY,ANY-method [[,EnvModules,ANY,ANY-method [[ [[ $,EnvModules-method available_modules,EnvModules-method coerce,EnvModules,list-method coerce,list,EnvModules-method default_modules,EnvModules-method EnvModules,EnvModules-method loaded_modules,EnvModules-method modulecmd,EnvModules-method names,EnvModules-method show,EnvModules-method

Class "EnvModules"

makeCATdb() GOHyperGAll() GOHyperGAll_Subset() GOHyperGAll_Simplify() GOCluster_Report() goBarplot()

GO term enrichment analysis for large numbers of gene sets

INTERSECTset-class as.list,INTERSECTset-method coerce,list,INTERSECTset-method complexitylevels,INTERSECTset-method intersectlist,INTERSECTset-method intersectmatrix,INTERSECTset-method length,INTERSECTset-method names,INTERSECTset-method setlist,INTERSECTset-method show,INTERSECTset-method

Class "INTERSECTset"

LineWise()

Class "LineWise"

printParam() subsetParam() replaceParam() renameParam() appendParam()

Accessories function to modify the Command-line Version 1

printParam2() appendParam2() replaceParam2() removeParam2() renameParam2()

Accessories function to modify the Command-line Version 2

SPRproject()

Workflow Project Initiation

SYSargs-class [,SYSargs,ANY,ANY,ANY-method coerce,list,SYSargs-method cores,SYSargs-method infile1,SYSargs-method infile2,SYSargs-method modules,SYSargs-method names,SYSargs-method length,SYSargs-method other,SYSargs-method results,SYSargs-method outfile1,SYSargs-method outpaths,SYSargs-method reference,SYSargs-method show,SYSargs-method software,SYSargs-method sysargs,SYSargs-method SampleName,SYSargs-method targetsheader,SYSargs-method targetsin,SYSargs-method targetsout,SYSargs-method

Class "SYSargs"

SYSargs2-class [,SYSargs2,ANY,ANY,ANY-method [[,SYSargs2,ANY,missing-method [[ [[ $,SYSargs2-method length,SYSargs2-method names,SYSargs2-method show,SYSargs2-method coerce,list,SYSargs2-method coerce,SYSargs2,list-method sysargs2 sysargs2,SYSargs2-method targets targets,SYSargs2-method targetsheader,SYSargs2-method modules modules,SYSargs2-method infile1,SYSargs2-method infile2,SYSargs2-method wf wf,SYSargs2-method clt clt,SYSargs2-method yamlinput,SYSargs2-method cmdlist,SYSargs2-method input input,SYSargs2-method output output,SYSargs2-method files files,SYSargs2-method inputvars inputvars,SYSargs2-method cmdToCwl cmdToCwl,SYSargs2-method status status,SYSargs2-method internal_outfiles internal_outfiles,SYSargs2-method baseCommand,SYSargs2-method SampleName,SYSargs2-method yamlinput yamlinput cmdToCwl cmdToCwl

Class "SYSargs2"

stepsWF() statusWF() targetsWF() outfiles() SE() dependency() projectInfo() runInfo() cmdlist() codeLine() SampleName() stepName() baseCommand() targetsheader() yamlinput() viewEnvir() copyEnvir() addResources() subset() getColumn() `appendStep<-`() `yamlinput<-`() `replaceStep<-`() `renameStep<-`() `dependency<-`() `appendCodeLine<-`() `replaceCodeLine<-`() `updateColumn<-`()

Class "SYSargsList"

SYSargsList()

SYSargsList Constructor

VENNset-class as.list,VENNset-method coerce,list,VENNset-method complexitylevels,VENNset-method intersectmatrix,VENNset-method length,VENNset-method names,VENNset-method setlist,VENNset-method show,VENNset-method vennlist,VENNset-method

Class "VENNset"

addAssay() addMetadata()

Extension accessor methods for SummarizedExperiment object

alignStats()

Alignment statistics

catDB-class catlist,catDB-method catmap,catDB-method coerce,list,catDB-method idconv,catDB-method names,catDB-method show,catDB-method

Class "catDB"

catmap()

catDB accessor methods

check.output() check.outfiles()

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

createParamFiles() writeParamFiles()

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

listCmdTools() listCmdModules()

List/check the existence of command-line tools of a workflow

loadWorkflow() renderWF() updateWF()

Constructs SYSargs2 object from CWL param and targets files

mergeBamByFactor()

Merge BAM files based on factor

module() moduleload() moduleUnload() modulelist() moduleAvail() moduleClear() moduleInit()

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() plotwfOutput() renderPlotwf()

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

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() seeFastqPlot()

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() targets.as.list()

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() combineVarReports() varSummary()

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