API for robertdouglasmorrison/DuffyTools
Duffy Lab Utility Tools

Global functions
AA3merFreq Source code
AAtoCodonOptimizedDNA Man page
AnnotationTable Man page
BScountPerML Man page
BScountToPctParasitemia Man page
CGIparse Source code
DESeq.DiffExpress Man page Source code
DKMshift Man page
DNAVtoAAV Man page Source code
DNAtoAA Man page Source code
DNAtoBestPeptide Man page
DNAtoFrameShiftingPeptides Man page
DuffyTools Man page
DuffyTools-package Man page
EdgeR.DiffExpress Man page Source code
ExonMap Man page
FileLineCount Man page
GeneMap Man page
HTMLheader Source code
HTMLincludeFile Source code
HTMLincludeText Source code
HTMLtable Source code
HTMLtableRow Source code
MapSets Man page
OptionsTable Man page
RankProduct.DiffExpress Man page
RrnaMap Man page
SAM.DiffExpress Man page Man page Source code
SAM.diffExpressRankOrder Man page
SeqMap Man page
Species Man page
Targets Man page
abline.segment Source code
addConfidenceLines Source code
addMapSet Man page
addOrigIDterms Source code
addTarget Man page
alias2Gene Man page
aliasGREP Man page
allowCompressedFileName Man page
as.AA3mers Source code
as.Fasta Man page
as.TRUEorFALSE Man page
as.link Source code
as.percent Man page
as.rankPercentile Man page
averageLineWithErrorBars Man page Source code
baseDepthTable Man page
baseDepthTableSubset Man page
baseDepthTableToVector Man page
baseDepthVector Man page
baseDepthVectorToTable Man page
bestAAreadingFrame Source code
bestMatchingFingerprint Source code
br Source code
calcRP Man page Source code
calcRandomGeneSetPvalues Source code
calcTM Man page
callBlast Man page
callBlastn Man page
callBlastp Man page
cellTypeExpression Source code
cgFraction Man page
checkDuffyPackages Man page
chromatogramInspector Source code
clipFastq Man page Source code
codonUsageFrequency Source code
colorBySpecies Man page
comments Source code
compareOneSignature Source code
consensusRank Man page
convertAApositionToGenomicDNAposition Man page
convertGenomicBasesToCodingAA Man page
convertGenomicDNAtoCodingDNA Man page
convertHypertext Man page Source code
diffExpressDistanceRankOrder Man page
diffExpressRankOrder Man page
do.QuSage Source code
duffy.ROC Source code
duffyMagnitudeNormalize Man page
duffyRMA Man page
duffyRMA.bgSubtract Man page
duffyRMA.qn Man page
elapsedProcTime Man page
emptyBaseDepthTable Man page
emptyBaseDepthVector Man page
enrichment Man page
enrichment.Nway Man page Source code
enrichment2html Source code
env.sub Man page Source code
errorBar Source code
exportCurrentMapSet Man page
exportTargets Man page
expressionCluster Man page
expressionFileSetToMatrix Man page
expressionHeatmap Man page
expressionMatrixToDElist Man page
expressionMatrixToFileSet Man page
expressionMatrixToMvalue Man page
factorBaseLocations Man page
fastAAreadingFrame Source code
fastSeqID2Species Man page
fastSeqPos2GenePos Man page
fastqPatternSearch Man page
fastqToFasta Man page
file.cleanSpecialCharactersFromFileName Man page
fileSet.PCAplot Source code
findSeqInChromatograms Source code
fit.gaussian Man page Man page Source code Source code
fit.gumbel Man page Source code Source code
fit.lorentzian Man page Source code Source code
fit.normal Man page Source code
fit.pulse Source code
fit.sine Source code
fit.triangleWave Source code
forestPlot Source code
gatherGeneSets Man page
gaussian Man page Man page Source code Source code
gene2Alias Man page
gene2Product Man page
gene2ProductAllSpecies Man page
geneSetAnalysis Man page
geneSetBestMatch Source code
geneSetDensity Man page
geneSetEnrichment Man page Source code
geneSetFitDataFrame Source code
geneSetHits Source code
geneSetHitsToPie Source code
geneSetMetaEnrichment Source code
geneSetOverlap Source code
geneSetPie Source code
getAllSpecies Man page
getAllSpeciesFilePrefixes Man page
getAllTargets Man page
getAnnotationTrue Man page
getAnnotationValue Man page
getCodonMap Man page
getCurrentExonMap Man page
getCurrentGeneMap Man page
getCurrentRrnaMap Man page
getCurrentSeqMap Man page
getCurrentSpecies Man page
getCurrentSpeciesFilePrefix Man page
getCurrentTarget Man page
getCurrentTargetFilePrefix Man page
getCurrentTargetSpecies Man page
getDensityKernelMode Man page
getFDRoneGeneSet Source code
getFastaSeqFromFilePath Man page
getFileLineCount Man page
getGlobalMetrics Man page
getHumanIDterms Man page
getOptionTrue Man page
getOptionValue Man page
getOtherSpeciesFilePrefix Man page
getSamplePairIDs Man page
getSpeciesFromSeqID Man page
getSpeciesText Man page
getVSAdomainMap Man page
getVSAgeneMap Man page
getVargeneDomainMap Man page
globalNormalize Man page
gumbel Man page Source code Source code
heatMapColors Source code Source code
hexDecode Source code
img Source code
importMapSet Man page
importTargets Man page
indentPrint Source code
levenshtein Man page Source code Source code
levenshteinDistanceMatrix Man page Source code Source code
lf Source code
lifeCycleExpression Source code
linkto Source code
loadFasta Man page
localityPlot Man page
logMeanPlusSD Man page Source code
logMedianPlusSD Man page Source code
logmean Man page Source code
lorentzian Man page Source code Source code
mailto Source code
makeGenePlotLinks Source code
makeInfoContentTable Source code
matrix.PCAplot Source code
merge.baseDepthTables Man page
mergeIntegerTables Man page
mergeTables Man page
metaEnrichment2html Source code
metaRank.data.frames Man page Source code
metaRank2html Man page Source code
metaRanks Man page Source code
metaResults Man page Source code
metaResultsToHTML Man page
molecularWeight Source code
movingAverage Man page Source code
multicore.by Man page
multicore.currentCoreCount Man page
multicore.lapply Man page Man page
multicore.samplePairs Man page Man page
multicore.setup Man page Man page
multicore.tapply Man page Man page
multicore.totalCoreCount Man page
myReverse Man page Source code
myReverseComplement Man page Source code
my_size_n_color Source code Source code
normal Man page Source code
oneDtable Man page Source code
openCompressedFile Man page
originalSamplePairID Man page
ortholog Man page
orthologSet Man page
p.combine Source code
p.combine.fisher Source code
p.combine.stouffer Source code
padStringWidth Source code
pctParasitemiaToBScount Man page
peptide.mergeOverlaps Source code
peptideChopper Source code
peptideRedundancySniffer Source code
peptideTable Source code
peptideTableSet Source code
peptideViewer Source code
phredScoreStringToInt Man page
pipe.GeneSetAnalysis Man page
pipe.GeneSetEnrichment Man page
plotChromatogramSet Source code
plotMetaResults Man page
plotRatios Man page
plotTranscripts Man page
pulse Source code
quickFileLineCountLookup Man page Source code
quickFileLineCountRecord Man page Source code
radial.plot Source code
rainbow Source code
rankEquivIntensity Man page
rankProduct Man page Source code
rankProductDiffExpress Man page Source code
readALN Man page Source code
readAnnotationTable Man page
readBlastOutput Man page
readFastq Man page
readNEXUS Man page Source code
readOptionsTable Man page
reduceMatrixToModules Source code
removeTempFolder Man page
scanText Source code
setCurrentSpecies Man page
setCurrentTarget Man page
shortGeneName Man page Source code
significantGenes Man page
simulate.enrichment.Nway Source code
sine Source code
spawnRcmd Man page
spline.line Source code
sqrtmean Man page Source code
sub.baseDepthTable Man page
sub.baseDepthTableSubset Man page
table2html Man page
tag Source code
tempFolder Man page
triangleWave Source code
tukey.biweight Man page Source code
tukey.logmean Man page Source code
tukey.mean Man page Source code
unitIntervalMA Man page Source code
untag Source code
validateMapSet Man page Source code
violinPlot Source code
vsaGeneProduct Man page
vsaTo3D7 Man page
webPNG Source code
whichAnnotationTrue Man page
wrap.text Source code
writeALN Man page
writeAsWebPage Source code
writeFasta Man page
writeFastq Man page
writeLongFasta Man page
writeRequestInfo Source code
robertdouglasmorrison/DuffyTools documentation built on Jan. 11, 2019, 5:38 p.m.