API for tgirke/systemPipeR
systemPipeR: NGS workflow and report generation environment

Global functions
$,SYSargs2-method Man page
$,SYSargs2Pipe-method Man page
.AffyID2GeneID Source code
.allAnnot Source code
.codingReport Source code
.gene2GOlist Source code
.getSRAfastq Source code
.readGOorg Source code
.resizeFeature Source code
.sampleDFgene2GO Source code
.subsetReadsByMappingRegion Source code
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
SYSargs2list Man page
SYSargs2list,SYSargs2-method Man page
SYSargs2list-method Man page
SYScreate 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
[,SYSargs,ANY,ANY,ANY-method Man page
[,SYSargs2,ANY,ANY,ANY-method Man page
[,SYSargs2Pipe,ANY,ANY,ANY-method Man page
[[,SYSargs2,ANY,missing-method Man page
[[,SYSargs2Pipe,ANY,ANY-method Man page
[[<-,SYSargs2,ANY,ANY,ANY-method Man page
[[<-,SYSargs2Pipe,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
avail_list Source code
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
clear Source code
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
coerce,SYSargs2,list-method Man page
coerce,SYSargs2Pipe,list-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,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
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
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
init 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
length,INTERSECTset-method Man page
length,SYSargs-method Man page
length,SYSargs2-method Man page
length,SYSargs2Pipe-method Man page
length,VENNset-method Man page
loadWF Man page
loadWorkflow Man page Source code
load_unload Source code
makeCATdb Man page Source code
mergeBamByFactor Man page Source code
module Man page Source code
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
nameUnnamed Source code
names,INTERSECTset-method Man page
names,SYSargs-method Man page
names,SYSargs2-method Man page
names,SYSargs2Pipe-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
plotfeatureCoverage Man page Source code
plotfeaturetypeCounts Man page Source code
populateCommandline Source code
predORF Man page Source code
preprocessReads Man page Source code
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
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
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,INTERSECTset-method Man page
show,SYSargs-method Man page
show,SYSargs2-method Man page
show,SYSargs2Pipe-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
subsetListbyName Source code
subsetWF Man page Source code
summary.WF Source code
summaryWF Man page
summaryWF,SYSargs2Pipe-method Man page
summaryWF-methods Man page
symLink2bam Man page Source code
sysargs Man page
sysargs,SYSargs-method Man page
sysargs-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
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
tgirke/systemPipeR documentation built on Nov. 8, 2019, 10:17 a.m.