Man pages for alexjgriffith/CCCA
Cross Condition ChIP Analyisis

addColnamesAdd Column Names
addFastaAdd Fasta
addNamesAdd Names
addRownamesAdd Row Names
andMand for Matrix
applyPeakPartitionsapply peak partitions
CCCACompare multiple ChIP data sets across experimental...
chromGenomeSortChrom Genome Sort
complimentreverse compliment
consenusIUPACConsensus IUPAC
convertChromsconvertChroms
createZipCreate Zip
distanceBetweenMotifsdistanceBetweenMoitfs
findMotifDistfind motif distance
findSharedRegionsFind Shared Regions
genEboxCombsGenerate Ebox Combinations
geneRangesGene Ranges
geneRangeToRegionGene Range to Region
generateGenerate
genomicRegionsGenomic Regions
genSwapFungenSwapFun
getDatagetData
getDistancegetDistance
getHeightsGet Heights
getMotifInfoGet Motif Info
getPileUpgetPileUp
greatGeneAssocGreat Gene Assoc
grepMotifsGrep Motifs
heightHistHeight Histrogram A plotting tool for histograms, Requires...
hg19Sorthg19Sort
histVisualizeVisualize batches of height data
homerWrapperHomer Wrapper
intersectNinstersect N
ispalandromeIs Palandrome
IUPACtoBaseTurn IUPAC lables into basic neucleotides
loadBedFileloadBedFile
loadPWMLoad PWM
locHistLocation Histogram A plotting tool for histograms, Requires...
locHist2locHist
lzipList Zip
makeAFSMake AFS
makeLogicMake Logical
makeTablemake table
mapziplistmap zip list
mLengthm Length
modulousmodulous
mormethod or
motifDistancesmotif distances
motifHistMotif histogram
motifs2ViewMotifs Two View
motifStringMotif String
multiPlotMulti Plot
mWidthm Width
nearSummitnearSummit
normalizeNormalize
numberIntersectIntersect Count
orderBedOrder Bed
orMorM
orsors
overlapOverlap
pairwiseCombspariwise Combinations
passPass
pcaPCA
peakPartitionspeak partitions
peakRegionspeak Regions #experimental
pileUpPileUp
plotPCsplot PCs
PWMtoConsPWM to Consensus Motif
qnQuantile Normalization
qstemQuick Stem Plot
rankChromsrankChroms
readCategoriesRead Categories
regionWrapperregion wrapper #experimental
reverseIUPACreverse IUPAC
sel2Select Second
sepAxisseperate axis
shiftFromZeroShift from zero
simpleSwapFunsimple swap fun
sortDataFramesort data frame
splitBlistSplit by List
splitZipSplit Zip
stemstem
stringToSwapstring to swap fun
unifyBedFileunify bed file
unionNunion N
unityOutputunity output
alexjgriffith/CCCA documentation built on June 3, 2017, 3:55 p.m.