Collection of (mostly bioinformatics) scripts that I use in day-to-day work
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AAI.rb
ANI.pl
Blast.rb
BlastXMLmerge.py
Btab.rb
CDP1802.rb
Chooser.rb
Cluster.rb
Codon.rb
CodonBias.rb
ColorGradient.rb
Colors.rb
DownloadGB.pl
GA.rb
GBfindOverlaps
GOS.rb
Gff.pm
GreenGenes.rb
Grid.rb
Histogram.rb
KarlinBias.rb
LZclusterbySite
MEPipeMakeClustersFromDNA
McCrowTree.rb
Mothur.rb
RogerBlast.rb
Silva.rb
Stats.rb
SuffixArray.rb
Taxonomy.rb
TigrGenBank.rb
WOA.rb
ZFile.rb
abundantKrakenLabels
add16SRogersSpreadsheet
addBangLang
addFastaAnnotation
addMappingIsotigs
addNonRedundantGB
addOtuInfo100MostWanted
addRPKMOrfAnnotationTab.jl
addSpeciesTaxonomy
addStrainTaxonomy
addTreePhylaColor
addqTreeInfo
alertTime
alg2transfac
aliasFasta
aliasNewick
alignFromBtab
alignHmm
alignReferencePhylodb
alignVariation
alignmentSummary
alphaNum
analyzeCombinedComboGos
annotateContigsBtab
annotateStephaneVenn
annotation-compare
arb2fasta
archiveProject
assembleSynCassettes
assemblyStats
autoFindTrees
azw2mobi
backAlign
bactBlastCluster
badgerBtab
bam2unmappedfq
bamKraken
bamSeqOverlap
barbHMPClusterSpreadsheet
batchCdhit
bed2geneCoords
bed2gtf
bedOverlap
bestHmmTbl
bestRecip
bigCat
bigCp
bigLS
bigMv
bigRm
binAlignPercentIdents
binBamReads
binBarcodedFasta
binBlastMatch
binPsoriasis
blast-contigs
blast2Combo
blast2GosTable
blast2table
blastClusterStruct
blastFindOnlyIn
blastLocalAllVsAll
blastSummary
blastSummaryPercentIdentity
blasthitCount
blastm82bed
btab
btab2Csv
btab2m8
buildAmphoraConcatAlignment
buildAnthony454ClusterInfo
buildAnthony454Info
buildAnthony454Spreadsheet
buildClassified16SDb
buildConcatAlignFromAlign
buildCuffGenesTable
buildFastaIndex
buildGOSCds
buildGenePresentAbsentMatrix
buildHmmConcatTM6
buildMclGroupsFromAli
buildOneWayVennCsv
buildOrthoAli
buildPathologic
buildPhyloAlias
buildPicrustTabFromMothurTaxSummary
buildReadAPISTable
buildRogerSpreadsheet
buildRoleCategoryFromGB
buildSigsTables
buildSilvaRef16SDb
buildTCGARsemTable
buildTCGATaxSummary
buildTCGATaxSummaryMetaphlan
buildTCGAmetadata
buildTaxItSeq_Info
buildTreesVenn
buildVennCsv
bulkSQLiteLoad
calcCAI
calcSeguid
cariMelayu
catBlast
cdhitParse
checkAffy
checkTrees
check_interleaved_fastq
circleClusterMap
classify16S
classifyAllHomologs
classifyBacMatches
classifyBestHomologs
classifyCategories
classifyComboBlast
classifyHmpSeqs
classifyMclClusters
classifyOrthologs
closestCorrelationCodon
cluster2APIS
cluster2CSV
clusterBtab
clusterDatabaseCSV
clusterMatrix
clusterPhy
clusterSearch
clusterSyn
cogTable
compOrfs
compare-orf-lists
compareBranches
compareBtabHits
compareCSV
compareCoords
compareECresults
compareGB
compareMooreComboDB
comparePanda
compareTopologies
compareUnmappedPeptides
completeTaxonomy
compressSnapMan
computeAAcomp
computeCodonBias
computeMUMI
computeN50
condor_muscle
contigSummarize
convertAlignment2Apis
convertClusteredStap
convertHyphoID
convertIDEAPositions
convertLocus
convertNCBI2APIS
convertPhatr2TranscriptCSV
convertPhyMLBootStraps
convertRDPgb
convertSTAP2ggdb
convertSilvaToGGFormat
copyApisTabsToDepot
copyGOSPep
copyNestedFiles
copyPeptidesFromTabFile
coreGenesAlignment
correlationCol
correlationContig
correlationOGT
cosmacasm
countBtabGeneHits
countCol
countGapsAlign
createArrayJob
createAtt
createComboLoadFromFasta
createCoverageListFromPromer
createGOSReadTaxTable
createHomologList
createIdeaAlignments
createMetaRepFromCSV
createSubLenFasta
createTabCommandsFromCSV
createTilingPseudoMolecule
createWikiPages
csFasta2XSQ
csv2xlsx
csvGrep
csvGrepList
csvPie
csvSQL
cx-al-unikodo
dataPartition
delEmptyApisBtab
deleteBlastNotInList
distribRun
dnaGrep
downloadAndProcessGDC
draftDNA2ComboBulk
dropShortFasta
dumpDB2tab
dumpMetaTrees
endoTable
ent2glim
entSearch
estimateMLBranchLengths
eukCoreCSV
eukcdhit
evaluateGlimmerStarts
evaluatePhymm
evaluateWebCarma
exonIntronCoverage
extractAPIS
extractBlastAlignments
extractBlastFasta
extractBlastOrfs
extractBtabHits
extractClark
extractClusters
extractCulturedGreenGenes
extractDownStreamGFF
extractECnumbers
extractGBcds
extractGFF
extractGreenGenesFromBodySites
extractGreenGenesFromHMPList
extractM8OnFasta
extractMclClusters
extractMultiBlastAlignments
extractORFSFromCoords
extractOnColumn
extractOnePerSpecies
extractOrthGroups
extractPairedUnMappedBamFastq
extractPanGenome
extractSeqMetaGenomeTaxId
extractTreeFromCSV
extractUpStreamGFF
extract_phylodb_annotation.pl
fact.elisp
fangking16S
fangking16Sextract
farthestClosestNeighborDist
fasta-matrix2transfac
fasta2Nexus
fasta2Phylip
fasta2Stockholm
fasta2clustalTree
fasta2fastq
fasta2rind
fastaAAcomp
fastaAAsubs
fastaAmbigRemove
fastaFunctionAdd
fastaGetColumn
fastaGrep
fastaGrepFile
fastaGrepList
fastaLengthHistogram
fastaSubSet
fastq2fasta
fastqKraken
fastq_pair_trim.pl
fastq_pos_quality.pl
fcsv.rb
fetchBart
fetchHmmCombo
fetchPhyloSeqs
fillOGT
filterAlignment
filterAlignmentsForIDEA
filterAmbigOrfs
filterClusterDist
filterFastaSize
filterFastq
filterGC
filterLowComplexity.py
filterLowEntropySeqs
filterM8Fasta
filterPairedFastq
filterPanMatrix
filterParalogsFindTrees
filterSmallOrfs
filterrRNAcsv
findApisSeq
findBootStrap
findCDS
findCloseGoldGenomes
findClosestApisMatch
findClosestMatchInDist
findCyanoAlphaInBlast
findEntOverlaps
findGoldSilva
findHighGC
findInfluenzaAA
findMatchingBtabHits
findNCBIPhyAnn
findNoTreeAPIS
findOnlyTrees
findOrfPos
findOrigin
findOrthGroups
findParalogs
findPepsInGenomes
findPosSites
findPrimer
findProfile
findReadsInScaffolds
findSamples
findSpeciesInSilva
findTreeRelatives
findTrees
findVibrioContam
findWOA
fixCSV
fixCondor
fixGenBankTblFrames
fixJ
fixJDB
fixJgiGFF
fixNAST
fixPairedReadsIllumina
fixPhylosift
fixPrefixTaxonomy
fixQIIMEMothurClass
fixScript
fixShortCon
fixTigrPlateIDs
gatherAncestral
gb2fasta
gb2gff
gbGetRNA
gbGrep
gbUpStream
gbfetch
gcHistogram
gcPhyloDB
gcskew
genbank2gff
genbank2tbl.py
genePair
generateCollabList
generateMultiAlignment
generateOrthologyTable
generateRandomProfile
generateSimExclude
generateVibrioTrees
genomeAlignment
genomeSizeCSV
genomeSummary
genomeTreeDist
get16STax
getAAfromdNdS
getCol
getFullLength
getGBCombo
getGBSpecies
getGosPeps
getKeggMaps
getNoHomologs
getProteinsPhylogenetically
getRibosomalProteins
getRibosomalRNA
getUnmappedReadsGDC
gff2gtf
gff2prot
gffSanityCheck
give_mumi.pl
glossMelayu
glossVolapuek
goFromGosClusterCSV
gosAbundCSV
gosBinPeps
gosClusterDistribution
gosClusterEnriched
gosFastaSqlLite
gosHmmDist
gosTaxGrpCSV
gosTaxPies
grabAlignPos
grabUrls
gtf2geneLength
gtfstats
heatmap
highqualProcess
histo-orf
histogram
hmmAli2Fasta
hmmAli2clustalTree
hmmParse
hmmRun
hmmRunSingle
hmmpfamFind
hmpDB
hmpRDP
idTaxaBySite
inPlaceReplace
indexFetch
inlineRubyTest
interleave_fastq
ionTorrentAlias
isogroupHistogram
iterate-critica
joinCSV
joinCuffDiff
joinRogerSeqs
jskel
kingdomSummarize
kitty
kittyNoEmpty
krakTable
labelCircTree
labelTaxaInfo
lhcProcessXLSX
libgenSearch
lineGrep
listPrevProteins
m8plus
m8toLCA
mac2unix
make-blastpairs
make16SDistTable
makeAffyGFF
makeBodySiteTrees
makeCircularGraph
makeCytoscapeGooglePies
makeECatt
makeEClist
makeGBatt
makeGC3fromCodonW
makeGOSLibraryBlasts
makeGOSLibraryFasta
makeGOSLibraryList
makeGTreeData
makeGitRemote
makeGlossary
makeGosPepBlast
makeHMPAlignment
makeHeatMapCsv
makeIPATHList
makeInfluenzaTable
makeLisaClusterTable
makeMapFromRecip
makeMepipeFromBtab
makeMetaDataLabels
makeMetabolicPoster
makePairedAlignments
makeParallelInferVariantsDada2
makePathoscopeTaxonTable
makePfam2Kog
makeSpSumFromFasta
makeStackedGraphCSV
makeSummaryReadsConditions
makeSybilAlignments
makeSynCassettes
makeTable
makeVizMapGB
makeWOAdb
makeregex
map-critica-orfs
mapBWA
mapHMP
mapMetaGene2JCVIPep
mapSilvaNCBItax
mapTopHat
matchKelpPrimers
matrixPan
mcast
mclHmmCSV
mclProcessBlast
mclSuperCSV
md2slides
mdaCdHitParse
mean
med2bib
mergeTables.jl
mergeYuzhen
metaGenePeps
mfoldFasta
minilisp
mitoProcess
modelTest
moranCsv
mothurAlignSeqs
mothurClassifySeqs
mothurCountMergeSample
mothurDistSeqs
mothurFilterSeqs
mothurPie
mothurScreenSeqs
mothurSummarySeqs
multiBlat
multirRNAAlign
myCoolJoin
myLatex2Html
nameTree
nasAinterpretBlast
ncbitaxID
neighborSummaryPie
noIndexFetch
noIndexGBFetch
nucWindow
oldSeqSummary
onePerSpeciesFasta
orfFinder
pHmmScan
pTmhmm
panNew
panStats
parseAAindex
parseAclame
parseApis
parseBACblast
parseBart
parseEST
parseEbook
parseGenBank2PhyloDB
parseHYPHY
parseHmmscan
parseKegg
parseKeggHierarchy
parseLisasProbeSet
parseMEPipeRst
parseMetaSimFna
parsePAML
parsePhoneBook
parseSTAP
parseSpSum
parseTIGRCoords
parseXLSX
pblastAllVsAll
pblastNCBI
pcr.seqs
pdf2epub
pepPhyloDistroGraph
percentBestBlastHits
pfam2go
phyloSummary
phyloTypeSummary
pickFromClusters
pickJumpStart
pickLongestFasta
pickOnePerOrgLisa
pickPhylaFastaList
pickRandomCsvEntries
pickRandomFastaEntries
pickRelatives
pickRepsFromTax
pieChart
plasmoAP
plot-dist
plotFastqQuality
plotFastqReadNum
posmapRarifaction
posmapStatistics
predictPathways
prepareDomClust
process454Directory
processClusterDist
processCoords
processGOSClusterForDB
processGOSHeaders
processGenomeQC
processHTMLAlign
processHomologList
processJoc
processJulie
processJumpStart
processLit
processMoran
processPTBlast
processPhyloDBSeqsTreeHeader
processProfile
processSafari
processSwissProt
processTopHatCounts
processWeightedPhylip
protGrep
prpsblast
pskel
ptTable
ptVenn
querySQL
rabundToDiversity
rbeautify
reOrderFasta
reRootBatch
readHitsCSV
readLenStats
readsNotInPosmap
recruitTree
recurseTaxonomy
reformatFasta
remove16SBlastFnaBtab
removeBadReadsFromList
removeContigsNotInPosmap
removeEmptyBLAST
removeFilteredBtab
removeIdentColumns
removeThirdBase
removeTooShortAlignSeqs
renameClusters
renameFastaOnFasta
renameFilesOnConversionPrefix
renameFilesOnTabAlias
renameInfluenzaFasta
renameLivingTree
renameMetatranscript
renameNestedFiles
renameORFS
renamePepSpec
renameSTAPOutput
renameSilvaLKT
reorderHeatColumns
reorderTable.jl
reorientTigrGenome
replaceCol
returnVennReps
riboOrder
rlisp2
rnaseqSQLprocess
rnaseqSQLreport
rnaseq_lib.rb
rskel
runBowtieMapping
runCluster
runCodeML
runCuffDiff
runEdgeR
runGBlocks
runGrid
runHoriz
runHybridAssembly
runMultiAaron
runProtTest
runQiime2
runTargetP
runTopHat
runTrimmomatic
sample_fastq.py
scaffoldDistance
scaffoldEnds
scaffoldInterpret
scaffoldSummary
scriptize
selectPrimers
selectTaxRepsCSV
sepOnFileFasta
separateFastaLengths
seqCompare
seqDBtoFasta
seqIdentity
setFastaOrigin
shredContigs
shuffleFasta
simSeq
simulateForwardReverse
simulateMarkers
simulateMatrix
simulateOtherUser
siteLister
sortFasta
specAlias
splitAlignment
splitApis
splitCSV
splitFasta
splitGOSPepOnLib
splitManifest
splitOnAccFasta
splitOnPattern
splitOnSpeciesFasta
splitOrthoFasta
splitPseudoMolecule
splitRhino
splitTransportDB
spritely
sqn2Fasta
stapNewickDraw
stapOrRdpPie
stitchFasta
stockholm2Fasta
sumCol
summarize454Barcode
summarizeAPISPhylaCounts.pl
summarizeApisContigs
summarizeAssembledSTAP
summarizeBlastParalogs
summarizeClusteredBlast
summarizeCoreGenesCSV
summarizeFindTrees
summarizeMetaTranBtab
summarizeMetatranscriptome
summarizeMoran
summarizeParalogBlasts
summarizePhylodb
summarizeRepeats
summarizeReptiles
summarizeSalinispora
summarizeSeqs
summarizeStarts
summarizeTranscripts
summarizeTrees
swarmNIHBlast
swarmNIHDiamond
swarmNIHHmmscan
swarmNIHKraken
swarmNIHTrimmomatic
sybil2IDEA
tab2csv
tabSum
table2pep
taxFileTest
taxIzeTree
tc_Newick.rb
tcgrep
testColors
thirdPosGC
timeLogicBlast
timeLogicFormatDB
timeq
top50MarkerSpecies
topBlast
topBlastDB
topBlastHits
topologizeTrees
trans_htab.pl
transfac2meme
translate
translate6frames
translateCDS
translateGlimmer
translateMarkerCSV
translateOrfs
transporterAnnotation
transporterSubstratesCSV
transporterSummary
treeApisTest
treeDistanceList
treeOutClusters
treeTest
treeinfo.pl
treeinfo2svg.pl
trimAlignment
trimPosAlignment
unAlias
unAliasFasta
unCluster
unencryptPDF
unidirectional2GenomePanGenome
unikodo-al-ch
unikodo-al-l3
unikodo-al-latex
uniqIPATH
uniqueifyAccs
uniqueifySeqs
upStream
updateReRunFastq
validateFastqFromMetadata
vennGenome
vennUnivenn
virtualPCR
wikipedia
wordSkew