A C F G I L M N O P Q R S T V W Y misc
alignStats | Alignment statistics |
as.list-method | Class '"INTERSECTset"' |
as.list-method | Class '"VENNset"' |
catDB-class | Class '"catDB"' |
catlist | catDB accessor methods |
catlist-method | Class '"catDB"' |
catlist-methods | catDB accessor methods |
catmap | catDB accessor methods |
catmap-method | Class '"catDB"' |
catmap-methods | catDB accessor methods |
clt | SYSargs2 accessor methods |
clt-method | Class '"SYSargs2"' |
clt-methods | SYSargs2 accessor methods |
clusterRun | Submit command-line tools to cluster |
cmdlist | SYSargs2 accessor methods |
cmdlist-method | Class '"SYSargs2"' |
cmdlist-methods | SYSargs2 accessor methods |
coerce-method | Class '"INTERSECTset"' |
coerce-method | Class '"SYSargs"' |
coerce-method | Class '"SYSargs2"' |
coerce-method | Class '"SYSargs2Pipe"' |
coerce-method | Class '"VENNset"' |
coerce-method | Class '"catDB"' |
combineVarReports | Generate Variant Report |
complexitylevels | Set Intersect and Venn Diagram Functions |
complexitylevels-method | Class '"INTERSECTset"' |
complexitylevels-method | Class '"VENNset"' |
complexitylevels-methods | Set Intersect and Venn Diagram Functions |
cores | SYSargs accessor methods |
cores-method | Class '"SYSargs"' |
cores-methods | SYSargs accessor methods |
countRangeset | Read counting for several range sets |
createWF | Constructs SYSargs2 object and creates CWL param files |
cwlfiles | SYSargs2 accessor methods |
cwlfiles-method | Class '"SYSargs2"' |
cwlfiles-methods | SYSargs2 accessor methods |
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 |
goBarplot | GO term enrichment analysis for large numbers of gene sets |
GOCluster_Report | GO term enrichment analysis for large numbers of gene sets |
GOHyperGAll | GO term enrichment analysis for large numbers of gene sets |
GOHyperGAll_Simplify | GO term enrichment analysis for large numbers of gene sets |
GOHyperGAll_Subset | GO term enrichment analysis for large numbers of gene sets |
idconv | catDB accessor methods |
idconv-method | Class '"catDB"' |
idconv-methods | catDB accessor methods |
infile1 | SYSargs accessor methods |
infile1-method | Class '"SYSargs"' |
infile1-method | Class '"SYSargs2"' |
infile1-methods | SYSargs accessor methods |
infile2 | SYSargs accessor methods |
infile2-method | Class '"SYSargs"' |
infile2-method | Class '"SYSargs2"' |
infile2-methods | SYSargs accessor methods |
input | SYSargs2 accessor methods |
input-method | Class '"SYSargs2"' |
input-methods | SYSargs2 accessor methods |
inputvars | SYSargs2 accessor methods |
inputvars-method | Class '"SYSargs2"' |
inputvars-methods | SYSargs2 accessor methods |
intersectlist | Set Intersect and Venn Diagram Functions |
intersectlist-method | Class '"INTERSECTset"' |
intersectlist-methods | Set Intersect and Venn Diagram Functions |
intersectmatrix | Set Intersect and Venn Diagram Functions |
intersectmatrix-method | Class '"INTERSECTset"' |
intersectmatrix-method | Class '"VENNset"' |
intersectmatrix-methods | Set Intersect and Venn Diagram Functions |
INTERSECTset-class | Class '"INTERSECTset"' |
length-method | Class '"INTERSECTset"' |
length-method | Class '"SYSargs"' |
length-method | Class '"SYSargs2"' |
length-method | Class '"SYSargs2Pipe"' |
length-method | Class '"VENNset"' |
loadWF | Constructs SYSargs2 object from CWL param and targets files |
loadWorkflow | Constructs SYSargs2 object from CWL param and targets files |
makeCATdb | GO term enrichment analysis for large numbers of gene sets |
mergeBamByFactor | Merge BAM files based on factor |
module | Interface to allow full use of the Environment Modules system for Unix |
modulelist | Interface to module system |
moduleload | Interface to module system |
modules | SYSargs accessor methods |
modules-method | Class '"SYSargs"' |
modules-method | Class '"SYSargs2"' |
modules-methods | SYSargs accessor methods |
names-method | Class '"INTERSECTset"' |
names-method | Class '"SYSargs"' |
names-method | Class '"SYSargs2"' |
names-method | Class '"SYSargs2Pipe"' |
names-method | Class '"VENNset"' |
names-method | Class '"catDB"' |
olBarplot | Bar plot for intersect sets |
olRanges | Identify Range Overlaps for IRanges and GRanges Object |
other | SYSargs accessor methods |
other-method | Class '"SYSargs"' |
other-methods | SYSargs accessor methods |
outfile1 | SYSargs accessor methods |
outfile1-method | Class '"SYSargs"' |
outfile1-methods | SYSargs accessor methods |
outpaths | SYSargs accessor methods |
outpaths-method | Class '"SYSargs"' |
outpaths-methods | SYSargs accessor methods |
output | SYSargs2 accessor methods |
output-method | Class '"SYSargs2"' |
output-methods | SYSargs2 accessor methods |
output_update | Updates the output files paths in the 'SYSargs2' object |
overLapper | Set Intersect and Venn Diagram Functions |
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 |
reference | SYSargs accessor methods |
reference-method | Class '"SYSargs"' |
reference-methods | SYSargs accessor methods |
renderWF | Populate all the command-line in an 'SYSargs2' object |
results | SYSargs accessor methods |
results-method | Class '"SYSargs"' |
results-methods | SYSargs accessor methods |
returnRPKM | RPKM Normalization |
runCommandline | Execute SYSargs and SYSargs2 |
runDiff | Differential abundance analysis for many range sets |
run_DESeq2 | Runs DESeq2 |
run_edgeR | Runs edgeR |
run_track | Keep track of the all 'SYSargs2' object |
SampleName | SYSargs accessor methods |
SampleName-method | Class '"SYSargs"' |
SampleName-methods | SYSargs accessor methods |
scaleRanges | Scale spliced ranges to genome coordinates |
seeFastq | Quality reports for FASTQ files |
seeFastqPlot | Quality reports for FASTQ files |
setlist | Set Intersect and Venn Diagram Functions |
setlist-method | Class '"INTERSECTset"' |
setlist-method | Class '"VENNset"' |
setlist-methods | Set Intersect and Venn Diagram Functions |
show-method | Class '"INTERSECTset"' |
show-method | Class '"SYSargs"' |
show-method | Class '"SYSargs2"' |
show-method | Class '"SYSargs2Pipe"' |
show-method | Class '"VENNset"' |
show-method | Class '"catDB"' |
software | SYSargs accessor methods |
software-method | Class '"SYSargs"' |
software-methods | SYSargs accessor methods |
subsetWF | Subsetting SYSargs2 class slots |
summaryWF | SYSargs2Pipe accessor methods |
summaryWF-method | Class '"SYSargs2Pipe"' |
summaryWF-methods | SYSargs2Pipe accessor methods |
symLink2bam | Symbolic links for IGV |
sysargs | SYSargs accessor methods |
SYSargs-class | Class '"SYSargs"' |
sysargs-method | Class '"SYSargs"' |
sysargs-methods | SYSargs accessor methods |
SYSargs2-class | Class '"SYSargs2"' |
SYSargs2list | SYSargs2 accessor methods |
SYSargs2list-method | Class '"SYSargs2"' |
SYSargs2list-method | SYSargs2 accessor methods |
SYSargs2Pipe-class | Class '"SYSargs2Pipe"' |
SYSargs2Pipe-method | SYSargs2Pipe accessor methods |
SYSargs2Pipe_ls | SYSargs2Pipe accessor methods |
SYSargs2Pipe_ls-method | Class '"SYSargs2Pipe"' |
systemArgs | Constructs SYSargs object from param and targets files |
targets | SYSargs2 accessor methods |
targets-method | Class '"SYSargs2"' |
targets-methods | SYSargs2 accessor methods |
targets.as.df | Convert targets list to data.frame |
targetsheader | SYSargs accessor methods |
targetsheader-method | Class '"SYSargs"' |
targetsheader-method | Class '"SYSargs2"' |
targetsheader-methods | SYSargs accessor methods |
targetsin | SYSargs accessor methods |
targetsin-method | Class '"SYSargs"' |
targetsin-methods | SYSargs accessor methods |
targetsout | SYSargs accessor methods |
targetsout-method | Class '"SYSargs"' |
targetsout-methods | SYSargs accessor methods |
track | SYSargs2Pipe accessor methods |
track-method | Class '"SYSargs2Pipe"' |
track-methods | SYSargs2Pipe accessor methods |
variantReport | Generate Variant Report |
varSummary | Generate Variant Report |
vennlist | Set Intersect and Venn Diagram Functions |
vennlist-method | Class '"VENNset"' |
vennlist-methods | Set Intersect and Venn Diagram Functions |
vennPlot | Plot 2-5 way Venn diagrams |
VENNset-class | Class '"VENNset"' |
wf | SYSargs2 accessor methods |
wf-method | Class '"SYSargs2"' |
wf-methods | SYSargs2 accessor methods |
WF_steps | SYSargs2Pipe accessor methods |
WF_steps-method | Class '"SYSargs2Pipe"' |
WF_steps-methods | SYSargs2Pipe accessor methods |
writeTargetsout | Write updated targets out to file |
writeTargetsRef | Generate targets file with reference |
yamlinput | SYSargs2 accessor methods |
yamlinput-method | Class '"SYSargs2"' |
yamlinput-methods | SYSargs2 accessor methods |
$-method | Class '"SYSargs2"' |
$-method | Class '"SYSargs2Pipe"' |
[-method | Class '"SYSargs"' |
[-method | Class '"SYSargs2"' |
[-method | Class '"SYSargs2Pipe"' |
[[-method | Class '"SYSargs2"' |
[[-method | Class '"SYSargs2Pipe"' |
[[<--method | Class '"SYSargs2"' |
[[<--method | Class '"SYSargs2Pipe"' |