bin/ucsc-shell
userapps/bin/aNotB
userapps/bin/addCols
userapps/bin/ave
userapps/bin/aveCols
userapps/bin/bamToPsl
userapps/bin/bedClip
userapps/bin/bedCommonRegions
userapps/bin/bedGeneParts
userapps/bin/bedGraphPack
userapps/bin/bedGraphToBigWig
userapps/bin/bedJoinTabOffset
userapps/bin/bedPileUps
userapps/bin/bedRemoveOverlap
userapps/bin/bedRestrictToPositions
userapps/bin/bedToBigBed
userapps/bin/bigBedInfo
userapps/bin/bigBedNamedItems
userapps/bin/bigBedSummary
userapps/bin/bigBedToBed
userapps/bin/bigWigAverageOverBed
userapps/bin/bigWigCat
userapps/bin/bigWigCluster
userapps/bin/bigWigCorrelate
userapps/bin/bigWigInfo
userapps/bin/bigWigMerge
userapps/bin/bigWigSummary
userapps/bin/bigWigToBedGraph
userapps/bin/bigWigToWig
userapps/bin/calc
userapps/bin/catDir
userapps/bin/catUncomment
userapps/bin/ccCp
userapps/bin/chopFaLines
userapps/bin/clusterMatrixToBarChartBed
userapps/bin/colTransform
userapps/bin/convolve
userapps/bin/countChars
userapps/bin/cpg_lh
userapps/bin/detab
userapps/bin/dnsInfo
userapps/bin/endsInLf
userapps/bin/faAlign
userapps/bin/faCmp
userapps/bin/faCount
userapps/bin/faFilter
userapps/bin/faFilterN
userapps/bin/faFlyBaseToUcsc
userapps/bin/faFrag
userapps/bin/faGapLocs
userapps/bin/faGapSizes
userapps/bin/faNcbiToUcsc
userapps/bin/faNoise
userapps/bin/faOneRecord
userapps/bin/faPolyASizes
userapps/bin/faRandomize
userapps/bin/faRc
userapps/bin/faRenameRecords
userapps/bin/faSimplify
userapps/bin/faSize
userapps/bin/faSomeRecords
userapps/bin/faSplit
userapps/bin/faToFastq
userapps/bin/faToNib
userapps/bin/faToTab
userapps/bin/faToTwoBit
userapps/bin/faTrans
userapps/bin/faTrimPolyA
userapps/bin/faTrimRead
userapps/bin/fastqStatsAndSubsample
userapps/bin/fastqToFa
userapps/bin/findMotif
userapps/bin/fixCr
userapps/bin/gapSplit
userapps/bin/gffPeek
userapps/bin/git-reports
userapps/bin/gmtime
userapps/bin/headRest
userapps/bin/htmlCheck
userapps/bin/htmlPics
userapps/bin/jkUniq
userapps/bin/lineCount
userapps/bin/linesToRa
userapps/bin/localtime
userapps/bin/mktime
userapps/bin/newProg
userapps/bin/newPythonProg
userapps/bin/nibFrag
userapps/bin/nibSize
userapps/bin/nt4Frag
userapps/bin/paraFetch
userapps/bin/paraSync
userapps/bin/pslLiftSubrangeBlat
userapps/bin/pslPosTarget
userapps/bin/pslRemoveFrameShifts
userapps/bin/pslScore
userapps/bin/pslToPslx
userapps/bin/pslToXa
userapps/bin/raSqlQuery
userapps/bin/raToLines
userapps/bin/raToTab
userapps/bin/randomLines
userapps/bin/rmFaDups
userapps/bin/rowsToCols
userapps/bin/scaffoldFaToAgp
userapps/bin/scrambleFa
userapps/bin/sizeof
userapps/bin/spacedToTab
userapps/bin/splitFile
userapps/bin/splitFileByColumn
userapps/bin/strexCalc
userapps/bin/stringify
userapps/bin/subChar
userapps/bin/subColumn
userapps/bin/subs
userapps/bin/tableSum
userapps/bin/tailLines
userapps/bin/textHist2
userapps/bin/textHistogram
userapps/bin/tickToDate
userapps/bin/toLower
userapps/bin/toUpper
userapps/bin/trackDbIndexBb
userapps/bin/twoBitDup
userapps/bin/twoBitInfo
userapps/bin/twoBitToFa
userapps/bin/udcCleanup
userapps/bin/undupFa
userapps/bin/upper
userapps/bin/vcfFilter
userapps/bin/venn
userapps/bin/verticalSplitSqlTable
userapps/bin/weedLines
userapps/bin/wigCorrelate
userapps/bin/wigToBigWig
userapps/bin/wordLine