API for scfurl/probedeeper
Making the Analysis of Microarray Data More Efficient

Global functions
AssignColors Source code
CalcDEAnalyzer Source code
ColObj.Subset Source code
ColObjCreate Source code
ColObjInit Source code
ComBat.SF Source code
EnrichmentPlot Source code
EnrichmentPlot.SF Source code
EnrichmentPlotLite Source code
ExtractLIMMA Source code
ExtractLimmaObj Source code
ExtractMCGO Source code
ExtractStats Source code
FindContrasts Source code Source code
GCTtoMAT Source code
GMTtoHM.list Source code
GMTtoHM.pdf Source code
GMTtoList Source code
GSEA Source code Source code
GSEA.Analyze.Sets Source code Source code
GSEA.ConsPlot Source code Source code
GSEA.EnrichmentScore Source code Source code
GSEA.EnrichmentScore2 Source code Source code
GSEA.Gct2Frame Source code Source code
GSEA.Gct2Frame2 Source code Source code
GSEA.GeneRanking Source code Source code
GSEA.HeatMapPlot Source code Source code
GSEA.HeatMapPlot2 Source code Source code
GSEA.NormalizeCols Source code Source code
GSEA.NormalizeRows Source code Source code
GSEA.ReadClsFile Source code Source code
GSEA.Res2Frame Source code Source code
GSEA.Threshold Source code Source code
GSEA.VarFilter Source code Source code
GSEA.write.gct Source code Source code
GroupSelection Source code
GroupSelectionLocal Source code
GroupSelectionNoLimma Source code
IPAtoGMT Source code
Input2DEAnalyzer Source code
IsAnnotated Source code
LEmatrix Source code
LightenDarkenColor Source code
LimmaObj2XL Source code
LimmaObjCreate Source code
MAboxplot Source code
MAboxplot2 Source code
MAboxplot3 Source code
MAboxplot7 Source code
MCGOContents Source code
MCGOpdf Source code
MultipleClassGSEA Source code Source code
OLD.GSEA.EnrichmentScore Source code Source code
PD.PCAplot Source code
PD.Subset Source code
PDVenn Source code
PDrunGSA Source code
PlotMultipleClassGSEAObject Source code
PlotMultipleEnrichmentPlots Source code
PreConsensusHM Source code
QuickGSEA Source code
RunGSEA Source code
SFHist Source code
SFVenn Source code
SFplot3D Source code
SigLevel Source code Source code
WriteGPFiles Source code
aka how to do it Man page
analyseMAdatalist Source code
annotatePerFile Source code
annotateProbes Source code
assignTypeDataFrame Source code
autoDAVID Source code
autoLIMMA Source code
autoLIMMA2DEAnalyzer Source code
breakup Source code
build.design Source code
clusterToGMT Source code
contrast.eq Source code
design.mat Source code
entrezdf Source code
exportNetwork.SF Source code
extractMAT Source code
findcommon Source code
fixrownames Source code
geneCorPlot Source code
getJobFiles Source code
gsea.heatmap.matrix Source code
gsea.read.gct Source code
gsea.write.cls Source code
gsea.write.gct Source code
gsea.write.gmt Source code
includeGenes Source code
int.eprior Source code
jgc Source code
loadGeoFile Source code
makeFootnote Source code Source code Source code
masterannotate Source code
matchTypes Source code
multiplot Source code
newGenePatternObject Source code
pdfplot Source code
quickVenn Source code
quickXL Source code
quickXL.list Source code
read.odf Source code
read.odfdata Source code
readColorFile Source code
readGMT.SF Source code
readGMTwitheset Source code
readautoLIMMA Source code
runDAVID Source code
runGO Source code
sliceColObj Source code
stats.table Source code
strwrap_strip_text Source code
synantag Source code
topDiffGenes Source code
writeDEAnalyzer Source code
writeMasterNetworkFile Source code
scfurl/probedeeper documentation built on Oct. 5, 2017, 10:57 a.m.