All functions

EnvModules-class

Class "EnvModules"

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

GO term enrichment analysis for large numbers of gene sets

INTERSECTset-class

Class "INTERSECTset"

SPRdata()

SPRdata

SYSargs-class

Class "SYSargs"

SYSargs2-class

Class "SYSargs2"

SYSargs2Pipe-class

Deprecated "SYSargs2Pipe" Class

SYSargs2Pipe_ls()

Deprecated "SYSargs2Pipe" accessor methods

SYSargsList-class

Class "SYSargsList"

VENNset-class

Class "VENNset"

addAssay() addMetadata()

Extension accessor methods for SummarizedExperiment object

alignStats()

Alignment statistics

catDB-class

Class "catDB"

catmap()

catDB accessor methods

clusterRun()

Submit command-line tools to cluster

config.param()

Adding param file

configWF()

Workflow Steps Selection

countRangeset()

Read counting for several range sets

createWF()

Constructs SYSargs2 object and creates CWL param 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

getQsubargs()

Arguments for qsub

initWF() initProject() SYSproject()

Workflow Project Initiation

loadWorkflow()

Constructs SYSargs2 object from CWL param and targets files

mergeBamByFactor()

Merge BAM files based on factor

module()

Interface to allow full use of the Environment Modules system for Unix

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

Interface to module system

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()

Graphviz Plot Workflow

plotfeatureCoverage()

Plot feature coverage results

plotfeaturetypeCounts()

Plot read distribution across genomic features

predORF()

Predict ORFs

preprocessReads()

Run custom read preprocessing functions

qsubRun()

Submit command-line tools to cluster

readComp()

Import sample comparisons from targets file

renderReport()

Render RMarkdown Report

renderWF()

Populate all the command-line in an SYSargs2 object

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

run_track()

Deprecated run_track functions

scaleRanges()

Scale spliced ranges to genome coordinates

seeFastq() seeFastqPlot()

Quality reports for FASTQ files

showDT()

Create an HTML table using DT package with fixed columns

subsetWF()

Subsetting SYSargs2 class slots

symLink2bam()

Symbolic links for IGV

sysargs()

SYSargs accessor methods

sysargs2()

SYSargs2 accessor methods

sysargslist()

SYSargsList accessor methods

systemArgs()

Constructs SYSargs object from param and targets files

targets.as.df()

Convert targets list to data.frame

tryCL()

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

writeTargetsRef()

Generate targets file with reference

writeTargetsout()

Write updated targets out to file