Index

A

addCluster() (in module trxtools.methods)

B

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

bed_split_strands() (in module trxtools.profiles.metaprofiles) binCollect3() (in module trxtools.profiles.profileTools) binMultipleMatrices() (in module trxtools.profiles.metaprofiles) boxplot1() (in module trxtools.plotting) bulkInputIDT() (in module trxtools.folding.assays)

C

calculateFDR() (in module trxtools.profiles.profileTools) calGC() (in module trxtools.methods) checkVienna() (in module trxtools.folding.secondary) chromosome2profile3end() (in module trxtools.sam.SAMgenome) cleanNames() (in module trxtools.methods) clusterClusterMap() (in module trxtools.plotting)

compare1toRef() (in module trxtools.profiles.profileTools) compareMoretoRef() (in module trxtools.profiles.profileTools) 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.profileTools)

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

F

filterExp() (in module trxtools.methods) find_pol3_terminators() (in module trxtools.methods) findPeaks() (in module trxtools.profiles.profileTools) findPrimer() (in module trxtools.folding.assays)

findTroughs() (in module trxtools.profiles.profileTools) Fold (class in trxtools.folding.nascent) foldingFromBigWig() (in module trxtools.profiles.BigWig) FoldingFromBigWig() (in module trxtools.profiles.profileTools) foldNascentElem() (in module trxtools.folding.nascent)

G

geneFromBigWig() (in module trxtools.profiles.BigWig) (in module trxtools.profiles.profileTools) geneFromBigWigTree() (in module trxtools.profiles.BigWig) generateSubplots() (in module trxtools.plotting) get_bw_data() (in module trxtools.profiles.metaprofiles) get_chrom_lens() (in module trxtools.profiles.metaprofiles) get_enrichment() (in module trxtools.tables.goEnrichment)

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

H

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

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

I

indexOrder() (in module trxtools.methods)

is_inside() (in module trxtools.methods)

J

join2d() (in module trxtools.folding.nascent)

join_strand_matrices() (in module trxtools.profiles.metaprofiles)

L

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

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

M

matrix_from_bigwig() (in module trxtools.profiles.metaprofiles) matrixFromBigWig() (in module trxtools.profiles.metaprofiles) matrixFromBigWigSparse() (in module trxtools.profiles.metaprofiles) merge2d() (in module trxtools.folding.nascent) metaprofile() (in module trxtools.profiles.metaprofiles) metaprofileAndHeatmap() (in module trxtools.plotting) module trxtools.folding.assays trxtools.folding.nascent trxtools.folding.secondary trxtools.methods trxtools.plotting trxtools.profiles.BigWig trxtools.profiles.metaprofiles trxtools.profiles.profileTools trxtools.sam.SAMgeneral trxtools.sam.SAMgenome trxtools.sam.SAMtranscripts trxtools.tables.goEnrichment

N

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

noncoded2profile() (in module trxtools.sam.SAMgeneral) noncoded2profile1() (in module trxtools.sam.SAMgeneral) nonTemplateDNA() (in module trxtools.folding.assays) normalize() (in module trxtools.methods) normalizeToLibrary() (in module trxtools.profiles.metaprofiles) ntotal() (in module trxtools.profiles.profileTools)

P

parseConcatFile() (in module trxtools.profiles.profileTools) parseCRACname() (in module trxtools.methods) parseFoldingName() (in module trxtools.folding.nascent) parseHeader() (in module trxtools.sam.SAMgenome) PCA() (in module trxtools.plotting) peak2matrice() (in module trxtools.profiles.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.folding.nascent) preprocess() (in module trxtools.profiles.profileTools) pseudocounts() (in module trxtools.profiles.profileTools)

Q

quantileCategory() (in module trxtools.methods)

R

randomDNAall() (in module trxtools.methods) randomDNAsingle() (in module trxtools.methods) read_bed() (in module trxtools.profiles.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.profiles.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.profiles.metaprofiles) reverse_complement() (in module trxtools.methods) reverse_complement_DNA() (in module trxtools.methods) reverse_complement_RNA() (in module trxtools.methods) RNAfold() (trxtools.folding.nascent.Fold method) RNAhybrid() (trxtools.folding.nascent.Hybrid method) RNAinvert() (trxtools.folding.nascent.Fold method) RNAinvertStall() (trxtools.folding.nascent.Fold method) rollingGC() (in module trxtools.methods) Rstem() (in module trxtools.folding.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.profileTools) 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.profiles.metaprofiles)

sequenceConstrain() (in module trxtools.folding.assays) slidingWindow() (in module trxtools.folding.nascent) stalled() (in module trxtools.folding.assays) strip_BigWig_names() (in module trxtools.profiles.BigWig) stripBigWignames() (in module trxtools.profiles.profileTools) stripCIGAR() (in module trxtools.sam.SAMgeneral) stripSubstitutions() (in module trxtools.sam.SAMgeneral) structureFile() (in module trxtools.folding.assays) substructures() (in module trxtools.folding.secondary)

T

templateDNA() (in module trxtools.folding.assays) test() (in module trxtools.folding.secondary) testScaffold() (in module trxtools.folding.assays) timestamp() (in module trxtools.methods) timestampRandomInt() (in module trxtools.methods) toOrder() (in module trxtools.folding.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) trim_bed() (in module trxtools.profiles.metaprofiles) trxtools.folding.assays module trxtools.folding.nascent module trxtools.folding.secondary module

trxtools.methods module trxtools.plotting module trxtools.profiles.BigWig module trxtools.profiles.metaprofiles module trxtools.profiles.profileTools module trxtools.sam.SAMgeneral module trxtools.sam.SAMgenome module trxtools.sam.SAMtranscripts module trxtools.tables.goEnrichment module

U

UNAfold() (trxtools.folding.nascent.Fold method)

V

vennDiagram() (in module trxtools.plotting)

vienna2format() (in module trxtools.folding.secondary)