Index

A

addCluster() (in module trxtools.methods)

analyseViennamarkGC() (in module trxtools.nascent)

B

bashCommand() (in module trxtools.methods) bashFolding() (trxtools.nascent.Fold method)

bashHybrid() (trxtools.nascent.Hybrid method) bulkInputIDT() (in module trxtools.assays)

C

calculateFDR() (in module trxtools.profiles) calGC() (in module trxtools.methods) checkVienna() (in module trxtools.secondary) chromosome2profile3end() (in module trxtools.SAMgenome) (in module trxtools.SAMgenome_old) cleanNames() (in module trxtools.methods)

clusterClusterMap() (in module trxtools.plotting) compare1toRef() (in module trxtools.profiles) compareMoretoRef() (in module trxtools.profiles) countDeletion() (in module trxtools.SAMgeneral) countMiddle() (in module trxtools.SAMgeneral) countRead() (in module trxtools.SAMgeneral)

D

define_experiments() (in module trxtools.methods)

dictBigWig() (in module trxtools.profiles)

E

expNameParser() (in module trxtools.methods) expStats() (in module trxtools.methods)

extendingWindow() (in module trxtools.nascent) extruded() (in module trxtools.assays)

F

filterExp() (in module trxtools.methods) findPeaks() (in module trxtools.profiles) findPrimer() (in module trxtools.assays)

findTroughs() (in module trxtools.profiles) Fold (class in trxtools.nascent) FoldingFromBigWig() (in module trxtools.profiles) foldNascentElem() (in module trxtools.nascent)

G

geneFromBigWig() (in module trxtools.profiles) get_enrichment() (in module trxtools.go_enrichment)

groupCIGAR() (in module trxtools.SAMgeneral) groupCRACsamples() (in module trxtools.methods)

H

handleInput() (in module trxtools.nascent) hplotSTARstats() (in module trxtools.plotting) hplotSTARstats_chimeric() (in module trxtools.plotting) hplotSTARstats_mapping() (in module trxtools.plotting)

hplotSTARstats_mistmatches() (in module trxtools.plotting) hplotSTARstats_readLen() (in module trxtools.plotting) hplotSTARstats_reads() (in module trxtools.plotting) Hybrid (class in trxtools.nascent)

I

indexOrder() (in module trxtools.methods)

J

join2d() (in module trxtools.nascent)

L

letterContent() (in module trxtools.methods) list_paths_in_current_dir() (in module trxtools.methods)

loops() (in module trxtools.secondary) loopStems() (in module trxtools.secondary) Lstem() (in module trxtools.secondary)

M

markVienna() (in module trxtools.nascent) merge2d() (in module trxtools.nascent) module trxtools.assays trxtools.go_enrichment trxtools.methods trxtools.nascent trxtools.plotting trxtools.profiles trxtools.SAMgeneral trxtools.SAMgenome trxtools.SAMgenome_old trxtools.SAMtranscripts trxtools.secondary

N

name2index() (in module trxtools.nascent) nascentElems() (in module trxtools.nascent) nascentElemsDataFrame() (in module trxtools.nascent) nascentFolding() (in module trxtools.nascent)

noncoded2profile() (in module trxtools.SAMgeneral) noncoded2profile1() (in module trxtools.SAMgeneral) nonTemplateDNA() (in module trxtools.assays) normalize() (in module trxtools.methods) ntotal() (in module trxtools.profiles)

P

parseConcatFile() (in module trxtools.profiles) parseCRACname() (in module trxtools.methods) parseFoldingName() (in module trxtools.nascent) parseHeader() (in module trxtools.SAMgenome) (in module trxtools.SAMgenome_old) parseNoncoded() (in module trxtools.SAMgeneral) parseNoncodedList() (in module trxtools.SAMgeneral) plot_as_box_plot() (in module trxtools.plotting) plot_diff() (in module trxtools.plotting) plot_heatmap() (in module trxtools.plotting) plot_to_compare() (in module trxtools.plotting)

plotCumulativePeaks() (in module trxtools.plotting) plotPCA() (in module trxtools.plotting) plotSTARstats() (in module trxtools.plotting) plotSTARstats_chimeric() (in module trxtools.plotting) plotSTARstats_mapping() (in module trxtools.plotting) plotSTARstats_mistmatches() (in module trxtools.plotting) plotSTARstats_readLen() (in module trxtools.plotting) plotSTARstats_reads() (in module trxtools.plotting) prepareNascent() (in module trxtools.nascent) preprocess() (in module trxtools.profiles) pseudocounts() (in module trxtools.profiles)

Q

quantileCategory() (in module trxtools.methods)

R

randomDNAall() (in module trxtools.methods) randomDNAsingle() (in module trxtools.methods) read_featureCount() (in module trxtools.methods) read_HTSeq_output() (in module trxtools.methods) read_list() (in module trxtools.methods) read_STARstats() (in module trxtools.methods) read_tabFile() (in module trxtools.methods) reads2genome() (in module trxtools.SAMgenome) (in module trxtools.SAMgenome_old) reads2genome3end() (in module trxtools.SAMgenome) (in module trxtools.SAMgenome_old) reads2genome5end() (in module trxtools.SAMgenome) (in module trxtools.SAMgenome_old)

reads2profile() (in module trxtools.SAMtranscripts) reads2profileDeletions() (in module trxtools.SAMtranscripts) readSalmon() (in module trxtools.methods) reverse_complement() (in module trxtools.methods) reverse_complement_DNA() (in module trxtools.methods) reverse_complement_RNA() (in module trxtools.methods) RNAfold() (trxtools.nascent.Fold method) RNAhybrid() (trxtools.nascent.Hybrid method) RNAinvert() (trxtools.nascent.Fold method) RNAinvertStall() (trxtools.nascent.Fold method) rollingGC() (in module trxtools.methods) Rstem() (in module trxtools.secondary) runPCA() (in module trxtools.methods)

S

sam2genome() (in module trxtools.SAMgenome) (in module trxtools.SAMgenome_old) sam2genome3end() (in module trxtools.SAMgenome_old) sam2genome5end() (in module trxtools.SAMgenome_old) sam2profiles() (in module trxtools.SAMtranscripts) save_csv() (in module trxtools.profiles) saveBigWig() (in module trxtools.SAMgeneral) selectEnds() (in module trxtools.SAMgeneral) selectFoldedN() (in module trxtools.nascent)

selectPolyA() (in module trxtools.SAMgeneral) selectSortPaths() (in module trxtools.SAMgeneral) sequenceConstrain() (in module trxtools.assays) slidingWindow() (in module trxtools.nascent) stalled() (in module trxtools.assays) stripBigWignames() (in module trxtools.profiles) stripCIGAR() (in module trxtools.SAMgeneral) stripSubstitutions() (in module trxtools.SAMgeneral) structureFile() (in module trxtools.assays) substructures() (in module trxtools.secondary)

T

templateDNA() (in module trxtools.assays) test() (in module trxtools.secondary) testScaffold() (in module trxtools.assays) timestamp() (in module trxtools.methods) timestampRandomInt() (in module trxtools.methods) toOrder() (in module trxtools.assays) tostripCIGARfive() (in module trxtools.SAMgeneral) tostripCIGARthree() (in module trxtools.SAMgeneral) transcript2profile() (in module trxtools.SAMtranscripts) transcript2profileDeletions() (in module trxtools.SAMtranscripts) trxtools.assays module trxtools.go_enrichment module trxtools.methods module

trxtools.nascent module trxtools.plotting module trxtools.profiles module trxtools.SAMgeneral module trxtools.SAMgenome module trxtools.SAMgenome_old module trxtools.SAMtranscripts module trxtools.secondary module

U

UNAfold() (trxtools.nascent.Fold method)

V

vienna2format() (in module trxtools.secondary)