API for systemPipeR
systemPipeR: NGS workflow and report generation environment

Global functions
$,EnvModules-method	Man page
$,SYSargs2-method	Man page
$,SYSargs2Pipe-method	Man page
$,SYSargsList-method	Man page
.AffyID2GeneID	Source code
.allAnnot	Source code
.checkOutArgs2	Source code
.codingReport	Source code
.gene2GOlist	Source code
.getSRAfastq	Source code
.makeBam	Source code
.readGOorg	Source code
.resizeFeature	Source code
.sampleDFgene2GO	Source code
.subsetReadsByMappingRegion	Source code
.sysargsrunCommandline	Source code
EnvModules,EnvModules-method	Man page
EnvModules-class	Man page
GOCluster_Report	Man page Source code
GOHyperGAll	Man page Source code
GOHyperGAll_Simplify	Man page Source code
GOHyperGAll_Subset	Man page Source code
INTERSECTset-class	Man page
SYSargs-class	Man page
SYSargs2-class	Man page
SYSargs2Pipe-class	Man page
SYSargs2Pipe-method	Man page
SYSargs2Pipe_ls	Man page
SYSargs2Pipe_ls,SYSargs2Pipe-method	Man page
SYSargs2_steps	Man page
SYSargs2_steps,SYSargsList-method	Man page
SYSargs2_steps-methods	Man page
SYSargsList-class	Man page
SYSproject	Man page Source code
SampleName	Man page
SampleName,SYSargs-method	Man page
SampleName-methods	Man page
VENNset-class	Man page
WF_steps	Man page
WF_steps,SYSargs2Pipe-method	Man page
WF_steps-methods	Man page
[,EnvModules,ANY,ANY,ANY-method	Man page
[,SYSargs,ANY,ANY,ANY-method	Man page
[,SYSargs2,ANY,ANY,ANY-method	Man page
[,SYSargs2Pipe,ANY,ANY,ANY-method	Man page
[,SYSargsList,ANY,ANY,ANY-method	Man page
[[,EnvModules,ANY,ANY-method	Man page
[[,EnvModules,ANY,missing-method	Man page
[[,SYSargs2,ANY,missing-method	Man page
[[,SYSargs2Pipe,ANY,ANY-method	Man page
[[,SYSargsList,ANY,ANY-method	Man page
[[<-,EnvModules,ANY,ANY,ANY-method	Man page
[[<-,EnvModules-method	Man page
[[<-,SYSargs2,ANY,ANY,ANY-method	Man page
[[<-,SYSargs2Pipe,ANY,ANY,ANY-method	Man page
[[<-,SYSargsList,ANY,ANY,ANY-method	Man page
alignStats	Man page Source code
as.list,INTERSECTset-method	Man page
as.list,VENNset-method	Man page
assembleCommandlineList	Source code
available_modules,EnvModules-method	Man page
catDB-class	Man page
catlist	Man page
catlist,catDB-method	Man page
catlist-methods	Man page
catmap	Man page
catmap,catDB-method	Man page
catmap-methods	Man page
clt	Man page
clt,SYSargs2-method	Man page
clt-methods	Man page
clusterRun	Man page Source code
cmdlist	Man page
cmdlist,SYSargs2-method	Man page
cmdlist-methods	Man page
codeSteps	Man page
codeSteps,SYSargsList-method	Man page
codeSteps-methods	Man page
coerce,EnvModules,list-method	Man page
coerce,SYSargs2,list-method	Man page
coerce,SYSargs2Pipe,list-method	Man page
coerce,SYSargsList,list-method	Man page
coerce,list,EnvModules-method	Man page
coerce,list,INTERSECTset-method	Man page
coerce,list,SYSargs-method	Man page
coerce,list,SYSargs2-method	Man page
coerce,list,SYSargs2Pipe-method	Man page
coerce,list,SYSargsList-method	Man page
coerce,list,VENNset-method	Man page
coerce,list,catDB-method	Man page
combineVarReports	Man page Source code
complexitylevels	Man page
complexitylevels,INTERSECTset-method	Man page
complexitylevels,VENNset-method	Man page
complexitylevels-methods	Man page
config.param	Man page
configWF	Man page Source code
cores	Man page
cores,SYSargs-method	Man page
cores-methods	Man page
countRangeset	Man page Source code
createWF	Man page Source code
cwlfiles	Man page
cwlfiles,SYSargs2-method	Man page
cwlfiles-methods	Man page
dataWF	Man page
dataWF,SYSargsList-method	Man page
dataWF-methods	Man page
default_modules,EnvModules-method	Man page
evalCode	Man page
featureCoverage	Man page Source code
featuretypeCounts	Man page Source code
filterDEGs	Man page Source code
filterVars	Man page
findBestMatch	Source code
genFeatures	Man page Source code
getQsubargs	Man page Source code
goBarplot	Man page Source code
idconv	Man page
idconv,catDB-method	Man page
idconv-methods	Man page
infile1	Man page
infile1,SYSargs-method	Man page
infile1,SYSargs2-method	Man page
infile1-methods	Man page
infile2	Man page
infile2,SYSargs-method	Man page
infile2,SYSargs2-method	Man page
infile2-methods	Man page
initProject	Man page Source code
initWF	Man page Source code
injectCommandlinelist	Source code
injectListbyName	Source code
input	Man page
input,SYSargs2-method	Man page
input-methods	Man page
inputvars	Man page
inputvars,SYSargs2-method	Man page
inputvars-methods	Man page
intersectlist	Man page
intersectlist,INTERSECTset-method	Man page
intersectlist-methods	Man page
intersectmatrix	Man page
intersectmatrix,INTERSECTset-method	Man page
intersectmatrix,VENNset-method	Man page
intersectmatrix-methods	Man page
is.modules.avail	Source code
length,INTERSECTset-method	Man page
length,SYSargs-method	Man page
length,SYSargs2-method	Man page
length,SYSargs2Pipe-method	Man page
length,SYSargsList-method	Man page
length,VENNset-method	Man page
loadWF	Man page
loadWorkflow	Man page Source code
loaded_modules,EnvModules-method	Man page
makeCATdb	Man page Source code
mergeBamByFactor	Man page Source code
module	Man page Source code
module.Clear.Init	Source code
module.List.Avail	Source code
module.Load.Unload	Source code
moduleAvail	Man page Source code
moduleClear	Man page Source code
moduleInit	Man page Source code
moduleUnload	Man page Source code
modulecmd,EnvModules-method	Man page
modulelist	Man page Source code
moduleload	Man page Source code
modules	Man page
modules,SYSargs-method	Man page
modules,SYSargs2-method	Man page
modules-methods	Man page
myEnvModules	Source code
nameUnnamed	Source code
names,EnvModules-method	Man page
names,INTERSECTset-method	Man page
names,SYSargs-method	Man page
names,SYSargs2-method	Man page
names,SYSargs2Pipe-method	Man page
names,SYSargsList-method	Man page
names,VENNset-method	Man page
names,catDB-method	Man page
nestedNames	Source code
olBarplot	Man page Source code
olRanges	Man page Source code
other	Man page
other,SYSargs-method	Man page
other-methods	Man page
outfile1	Man page
outfile1,SYSargs-method	Man page
outfile1-methods	Man page
outpaths	Man page
outpaths,SYSargs-method	Man page
outpaths-methods	Man page
output	Man page
output,SYSargs2-method	Man page
output-methods	Man page
output_update	Man page Source code
overLapper	Man page Source code
pathInstance	Source code
pathUtils	Source code
plotWF	Man page
plotfeatureCoverage	Man page Source code
plotfeaturetypeCounts	Man page Source code
populateCommandline	Source code
predORF	Man page Source code
preprocessReads	Man page Source code
projectWF	Man page
projectWF,SYSargsList-method	Man page
projectWF-methods	Man page
qsubRun	Man page Source code
readComp	Man page Source code
reference	Man page
reference,SYSargs-method	Man page
reference-methods	Man page
renderCommandline	Source code
renderInputs	Source code
renderOutputs	Source code
renderReport	Man page Source code
renderWF	Man page Source code
results	Man page
results,SYSargs-method	Man page
results-methods	Man page
returnRPKM	Man page Source code
runCommandline	Man page Source code
runDiff	Man page Source code
runWF	Man page Source code
run_DESeq2	Man page Source code
run_edgeR	Man page Source code
run_track	Man page Source code
scaleRanges	Man page Source code
seeFastq	Man page Source code
seeFastqPlot	Man page Source code
setlist	Man page
setlist,INTERSECTset-method	Man page
setlist,VENNset-method	Man page
setlist-methods	Man page
show,EnvModules-method	Man page
show,INTERSECTset-method	Man page
show,SYSargs-method	Man page
show,SYSargs2-method	Man page
show,SYSargs2Pipe-method	Man page
show,SYSargsList-method	Man page
show,VENNset-method	Man page
show,catDB-method	Man page
software	Man page
software,SYSargs-method	Man page
software-methods	Man page
statusWF	Man page
statusWF,SYSargsList-method	Man page
statusWF-methods	Man page
stepsWF	Man page
stepsWF,SYSargsList-method	Man page
stepsWF-methods	Man page
subsetListbyName	Source code
subsetRmd	Source code
subsetWF	Man page Source code
summary.WF	Source code
summaryWF	Man page
summaryWF,SYSargs2Pipe-method	Man page
summaryWF,SYSargsList-method	Man page
summaryWF-methods	Man page
symLink2bam	Man page Source code
sysargs	Man page
sysargs,SYSargs-method	Man page
sysargs-methods	Man page
sysargs2	Man page
sysargs2,SYSargs2-method	Man page
sysargs2-method	Man page
sysargslist	Man page
sysargslist,SYSargsList-method	Man page
sysargslist-method	Man page
sysconfig	Man page
sysconfig,SYSargsList-method	Man page
sysconfig-methods	Man page
systemArgs	Man page Source code
targets	Man page
targets,SYSargs2-method	Man page
targets-methods	Man page
targets.as.df	Man page Source code
targets.as.list	Source code
targetsheader	Man page
targetsheader,SYSargs-method	Man page
targetsheader,SYSargs2-method	Man page
targetsheader-methods	Man page
targetsin	Man page
targetsin,SYSargs-method	Man page
targetsin-methods	Man page
targetsout	Man page
targetsout,SYSargs-method	Man page
targetsout-methods	Man page
termMMatch	Source code
track	Man page
track,SYSargs2Pipe-method	Man page
track-methods	Man page
trackWF	Source code
tryCL	Man page
tryPath	Man page
varSummary	Man page Source code
variantReport	Man page
vennPlot	Man page Source code
vennlist	Man page
vennlist,VENNset-method	Man page
vennlist-methods	Man page
wf	Man page
wf,SYSargs2-method	Man page
wf-methods	Man page
write.clt	Source code
write.yml	Source code
writeTargetsRef	Man page Source code
writeTargetsout	Man page
yamlinput	Man page
yamlinput,SYSargs2-method	Man page
yamlinput-methods	Man page