Difference between revisions of "KentUtils"
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Latest revision as of 14:05, 15 June 2017
Introduction
A myriad of bioinformatics tools from Jim Kent
The tools
addCols bedGraphToBigWig bigWigCorrelate chainStitchId faCmp featureBits hgFindSpec linesToRa mafToAxt paraFetch pslSort spacedToTab validateFiles ameme bedIntersect bigWigInfo chainSwap faCount fetchChromSizes hgGcPercent localtime mafToPsl paraSync pslStats splitFile validateManifest autoDtd bedItemOverlapCount bigWigMerge chainToAxt faFilter findMotif hgLoadBed mafAddIRows makeTableList positionalTblCheck pslSwap splitFileByColumn wigCorrelate autoSql bedPileUps bigWigSummary chainToPsl faFilterN gapToLift hgLoadOut mafAddQRows maskOutFa pslCat pslToBed sqlToXml wigEncode autoXml bedRemoveOverlap bigWigToBedGraph checkAgpAndFa faFrag genePredCheck hgLoadWiggle mafCoverage mktime pslCDnaFilter pslToChain stringify wigToBigWig ave bedRestrictToPositions bigWigToWig checkCoverageGaps faNoise genePredHisto hgsql mafFetch mrnaToGene pslCheck pslToPslx subChar wordLine aveCols bedSort blastToPsl checkHgFindSpec faOneRecord genePredSingleCover hgsqldump mafFilter netChainSubset pslDropOverlap pslxToFa subColumn xmlCat axtChain bedToBigBed blastXmlToPsl checkTableCoords faPolyASizes genePredToBed hgTrackDb mafFrag netClass pslFilter qacAgpLift tailLines xmlToSql axtSort bedToExons calc chopFaLines faRandomize genePredToFakePsl hgWiggle mafFrags netFilter pslHisto qacToQa tdbQuery axtSwap bedToGenePred catDir chromGraphFromBin faRc genePredToGtf htmlCheck mafGene netSplit pslLiftSubrangeBlat qacToWig textHistogram axtToMaf bedToPsl catUncomment chromGraphToBin faSize genePredToMafFrames hubCheck mafMeFirst netSyntenic pslMap qaToQac tickToDate axtToPsl bedWeedOverlapping chainAntiRepeat colTransform faSomeRecords gfClient ixIxx mafOrder netToAxt pslMrnaCover randomLines toLower bedClip bigBedInfo chainFilter countChars faSplit gff3ToGenePred lavToAxt mafRanges netToBed pslPairs raSqlQuery toUpper bedCommonRegions bigBedNamedItems chainMergeSort crTreeIndexBed fastqToFa gff3ToPsl lavToPsl mafsInRegion newProg pslPartition raToLines trfBig bedCoverage bigBedSummary chainNet crTreeSearchBed faToFastq gfServer ldHgGene mafSpeciesList nibFrag pslPretty raToTab twoBitDup bedExtendRanges bigBedToBed chainPreNet dbSnoop faToTab gmtime liftOver mafSpeciesSubset nibSize pslRecalcMatch rmFaDups twoBitInfo bedGeneParts bigWigAverageOverBed chainSort dbTrash faToTwoBit gtfToGenePred liftOverMerge mafSplit oligoMatch pslReps rowsToCols twoBitMask bedGraphPack bigWigCat chainSplit estOrient faTrans headRest liftUp mafSplitPos overlapSelect pslSelect sizeof twoBitToFa
