Index

A

addCluster() (in module trxtools.methods)

B

bashCommand() (in module trxtools.methods) bashFolding() (trxtools.nascent.Fold method) bashHybrid() (trxtools.nascent.Hybrid method) bed2len() (in module trxtools.methods)

bed_split_strands() (in module trxtools.metaprofiles) binCollect3() (in module trxtools.profiles) binMultipleMatrices() (in module trxtools.metaprofiles) boxplot1() (in module trxtools.plotting) 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.sam.SAMgenome) cleanNames() (in module trxtools.methods) clusterClusterMap() (in module trxtools.plotting)

compare1toRef() (in module trxtools.profiles) compareMoretoRef() (in module trxtools.profiles) countDeletion() (in module trxtools.sam.SAMgeneral) countMiddle() (in module trxtools.sam.SAMgeneral) countRead() (in module trxtools.sam.SAMgeneral) cumulativeDifference() (in module trxtools.plotting) cumulativePeaks() (in module trxtools.plotting)

D

define_experiments() (in module trxtools.methods) dictBigWig() (in module trxtools.profiles)

DNA_stretch_positions() (in module trxtools.methods) DNA_string_positions() (in module trxtools.methods)

E

enhancedVolcano() (in module trxtools.plotting) enriched() (in module trxtools.methods) 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) find_pol3_terminators() (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.BigWig) FoldingFromBigWig() (in module trxtools.profiles) foldNascentElem() (in module trxtools.nascent)

G

geneFromBigWig() (in module trxtools.BigWig) (in module trxtools.profiles) generateSubplots() (in module trxtools.plotting) get_bw_data() (in module trxtools.metaprofiles) get_enrichment() (in module trxtools.go_enrichment) get_multiple_matrices() (in module trxtools.metaprofiles)

getMultipleMatrices() (in module trxtools.metaprofiles) getMultipleMatricesFromPeak() (in module trxtools.metaprofiles) getSeqData() (in module trxtools.BigWig) GOterm() (in module trxtools.plotting) groupCIGAR() (in module trxtools.sam.SAMgeneral) groupCRACsamples() (in module trxtools.methods)

H

handleInput() (in module trxtools.nascent) hplotSTARstats_readLen() (in module trxtools.plotting)

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

I

indexOrder() (in module trxtools.methods)

is_inside() (in module trxtools.methods)

J

join2d() (in module trxtools.nascent)

join_strand_matrices() (in module trxtools.metaprofiles)

L

letterContent() (in module trxtools.methods) listPaths() (in module trxtools.methods) loadGTF() (in module trxtools.methods)

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

M

matrix_from_bigwig() (in module trxtools.metaprofiles) matrixFromBigWig() (in module trxtools.metaprofiles) merge2d() (in module trxtools.nascent) metaprofile() (in module trxtools.metaprofiles) metaprofileAndHeatmap() (in module trxtools.plotting) module trxtools.assays trxtools.BigWig trxtools.go_enrichment trxtools.metaprofiles trxtools.methods trxtools.nascent trxtools.plotting trxtools.profiles trxtools.sam.SAMgeneral trxtools.sam.SAMgenome trxtools.sam.SAMtranscripts trxtools.secondary

N

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

noncoded2profile() (in module trxtools.sam.SAMgeneral) noncoded2profile1() (in module trxtools.sam.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.sam.SAMgenome) PCA() (in module trxtools.plotting) peak2matrice() (in module trxtools.metaprofiles) 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)

plotAndFolding() (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_bed() (in module trxtools.metaprofiles) read_DEseq() (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) readBED() (in module trxtools.metaprofiles) reads2genome() (in module trxtools.sam.SAMgenome) reads2genome3end() (in module trxtools.sam.SAMgenome) reads2genome5end() (in module trxtools.sam.SAMgenome) reads2genomeDeletions() (in module trxtools.sam.SAMgenome)

reads2profile() (in module trxtools.sam.SAMtranscripts) reads2profileDeletions() (in module trxtools.sam.SAMtranscripts) readSalmon() (in module trxtools.methods) regionScore() (in module trxtools.metaprofiles) 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.sam.SAMgenome) sam2profiles() (in module trxtools.sam.SAMtranscripts) save_csv() (in module trxtools.profiles) saveBigWig() (in module trxtools.sam.SAMgeneral) select_colors() (in module trxtools.plotting) selectEnds() (in module trxtools.sam.SAMgeneral) selectNoncodedAndProfile() (in module trxtools.sam.SAMgeneral) selectSortPaths() (in module trxtools.sam.SAMgeneral) selectSubsetMM() (in module trxtools.metaprofiles)

sequenceConstrain() (in module trxtools.assays) slidingWindow() (in module trxtools.nascent) stalled() (in module trxtools.assays) strip_BigWig_names() (in module trxtools.BigWig) stripBigWignames() (in module trxtools.profiles) stripCIGAR() (in module trxtools.sam.SAMgeneral) stripSubstitutions() (in module trxtools.sam.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.sam.SAMgeneral) tostripCIGARthree() (in module trxtools.sam.SAMgeneral) transcript2profile() (in module trxtools.sam.SAMtranscripts) transcript2profileDeletions() (in module trxtools.sam.SAMtranscripts) trxtools.assays module trxtools.BigWig module trxtools.go_enrichment module trxtools.metaprofiles module

trxtools.methods module trxtools.nascent module trxtools.plotting module trxtools.profiles module trxtools.sam.SAMgeneral module trxtools.sam.SAMgenome module trxtools.sam.SAMtranscripts module trxtools.secondary module

U

UNAfold() (trxtools.nascent.Fold method)

V

vennDiagram() (in module trxtools.plotting)

vienna2format() (in module trxtools.secondary)