API for JokingHero/ORFik
Open Reading Frames in Genomics

Global functions
ORFik Man page
ORFik-package Man page
addCdsOnLeaderEnds Man page Source code
addNewTSSOnLeaders Man page Source code
asTX Man page Source code
assignAnnotations Man page Source code
assignFirstExonsStartSite Man page Source code
assignLastExonsStopSite Man page Source code
assignTSSByCage Man page Source code
bedToGR Man page Source code
changePointAnalysis Man page Source code
checkRFP Man page Source code
checkRNA Man page Source code
codonSumsPerGroup Man page Source code
computeFeatures Man page Source code
computeFeaturesCage Man page Source code
convertToOneBasedRanges Man page Source code
coverageByWindow Man page Source code
coveragePerTiling Man page Source code
defineIsoform Man page Source code
defineTrailer Man page Source code
detectRibosomeShifts Man page Source code
disengagementScore Man page Source code
distToCds Man page Source code
distToTSS Man page Source code
downstreamFromPerGroup Man page Source code
downstreamN Man page Source code
downstreamOfPerGroup Man page Source code
entropy Man page Source code
extendLeaders Man page Source code
extendsTSSexons Man page Source code
filterCage Man page Source code
findCageUTRFivelen Man page Source code
findFa Man page Source code
findMapORFs Man page Source code
findMaxPeaks Man page Source code
findNewTSS Man page Source code
findORFs Man page Source code
findORFsFasta Man page Source code
findORFs_fasta Source code
firstEndPerGroup Man page Source code
firstExonPerGroup Man page Source code
firstStartPerGroup Man page Source code
floss Man page Source code
fpkm Man page Source code
fpkm_calc Man page Source code
fractionLength Man page Source code
fread.bed Man page Source code
gSort Man page Source code
getStartStopWindows Man page Source code
groupGRangesBy Man page Source code
hasHits Man page Source code
initiationScore Man page Source code
insideOutsideORF Man page Source code
is.gr_or_grl Man page Source code
is.grl Man page Source code
isInFrame Man page Source code
isOverlapping Man page Source code
isPeriodic Man page Source code
kozakSequenceScore Man page Source code
lastExonEndPerGroup Man page Source code
lastExonPerGroup Man page Source code
lastExonStartPerGroup Man page Source code
longestORFs Man page Source code
makeExonRanks Man page Source code
makeORFNames Man page Source code
mapToGRanges Man page Source code
matchNaming Man page Source code
metaWindow Man page Source code
numExonsPerGroup Man page Source code
orfID Man page Source code
orfScore Man page Source code
orfs_as_IRanges Source code
orfs_as_List Source code
overlapsToCoverage Man page Source code
parseCigar Man page Source code
pmapFromTranscriptF Man page Source code
rankOrder Man page Source code
readWidths Man page Source code
reassignTSSbyCage Man page Source code
reassignTxDbByCage Man page Source code
reduceKeepAttr Man page Source code
regroupRleList Man page Source code
remakeTxdbExonIds Man page Source code
removeMetaCols Man page Source code
removeTxdbExons Man page Source code
restrictTSSByUpstreamLeader Man page Source code
riboTISCoverageProportion Man page Source code
ribosomeReleaseScore Man page Source code
ribosomeStallingScore Man page Source code
seqnamesPerGroup Man page Source code
shiftFootprints Man page Source code
sortPerGroup Man page Source code
startCodons Man page Source code
startDefinition Man page Source code
startRegionString Man page Source code
startSites Man page Source code
stopCodons Man page Source code
stopDefinition Man page Source code
stopSites Man page Source code
strandBool Man page Source code
strandPerGroup Man page Source code
subsetCoverage Man page Source code
subset_to_frame Man page Source code
tile1 Man page Source code
translationalEff Man page Source code
txLen Man page Source code
txNames Man page Source code
txNamesWithLeaders Man page Source code
txSeqsFromFa Man page Source code
uORFSearchSpace Man page Source code
uniqueGroups Man page Source code
uniqueOrder Man page Source code
unlistGrl Man page Source code
updateTxdbRanks Man page Source code
updateTxdbStartSites Man page Source code
upstreamFromPerGroup Man page Source code
upstreamOfPerGroup Man page Source code
validGRL Man page Source code
widthPerGroup Man page Source code
windowPerGroup Man page Source code
JokingHero/ORFik documentation built on Oct. 17, 2018, 4:10 p.m.