Index

_

__contains__() (pytransit.tnseq_tools.Genes method), [1] __eq__() (pytransit.tnseq_tools.Gene method), [1] __getitem__() (pytransit.tnseq_tools.Gene method), [1] (pytransit.tnseq_tools.Genes method), [1]

__len__() (pytransit.tnseq_tools.Genes method), [1] __lt__() (pytransit.tnseq_tools.Gene method), [1] __str__() (pytransit.tnseq_tools.Gene method), [1] (pytransit.tnseq_tools.Genes method), [1]

A

aboutFunc() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) AdaptiveBGCNorm (class in pytransit.norm_tools), [1] add_file() (pytransit.analysis.base.AnalysisMethod method) addFeatureFunc() (pytransit.trash.TrashFrame method) (pytransit.view_trash.MainFrame method) addFile() (pytransit.transit_gui.TnSeekFrame method) addFileFunc() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) addPlots() (pytransit.qcDisplay.qcFrame method) allSelected() (pytransit.transit_gui.TnSeekFrame method) allViewFunc() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) AnalysisGUI (class in pytransit.analysis.base) AnalysisMethod (class in pytransit.analysis.base)

annotationFileFunc() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) annotationGFF3_to_PT() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) annotationPT_to_GFF3() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) annotationPT_to_PTT() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) annotationPTT_to_PT() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) AnovaAnalysis (class in pytransit.analysis.anova) AnovaMethod (class in pytransit.analysis.anova) AssumeZerosDialog (class in pytransit.transit_gui) (class in pytransit.transit_tools), [1] aton() (in module pytransit.transit_tools), [1] AutoResizeCols() (pytransit.fileDisplay.TransitGridFrame method)

B

backward_procedure() (pytransit.analysis.hmm.HMMMethod method) basename() (in module pytransit.transit_tools), [1] bayesian_ess_thresholds() (in module pytransit.stat_tools), [1] BetaGeomNorm (class in pytransit.norm_tools), [1] bFDR() (in module pytransit.stat_tools), [1] BH_fdr_correction() (in module pytransit.stat_tools), [1] binom() (in module pytransit.stat_tools), [1]

binom_cdf() (in module pytransit.stat_tools), [1] binom_test() (in module pytransit.stat_tools), [1] BinomialAnalysis (class in pytransit.analysis.binomial) BinomialFile (class in pytransit.analysis.binomial) BinomialGUI (class in pytransit.analysis.binomial) BinomialMethod (class in pytransit.analysis.binomial) boxcoxTable() (in module pytransit.stat_tools), [1] boxcoxtransform() (in module pytransit.stat_tools), [1]

C

calc_overlap() (pytransit.analysis.tn5gaps.Tn5GapsMethod method) calcLFCs() (pytransit.analysis.anova.AnovaMethod method) calculate_pins() (pytransit.analysis.hmm.HMMMethod method) changedMaxFunc() (pytransit.trash.TrashFrame method) (pytransit.view_trash.MainFrame method) check_wig_includes_zeros() (in module pytransit.tnseq_tools), [1] checkHMMFeature() (pytransit.trash.TrashFrame method) chooseNormalization() (pytransit.transit_gui.TnSeekFrame method) choseMethodsMenu() (pytransit.transit_gui.TnSeekFrame method) classify() (pytransit.analysis.gumbel.GumbelMethod method) cleanargs() (in module pytransit.transit_tools), [1] cleaninfgeom() (in module pytransit.norm_tools), [1] (pytransit.norm_tools.AdaptiveBGCNorm method), [1] (pytransit.norm_tools.BetaGeomNorm method), [1] clearStatus() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) (pytransit.trash.TrashFrame method) (pytransit.view_trash.MainFrame method) comb() (in module pytransit.stat_tools), [1]

comb1() (in module pytransit.stat_tools), [1] combine_lib_dicts() (in module pytransit.stat_tools), [1] combine_replicates() (in module pytransit.tnseq_tools), [1] console_message() (pytransit.analysis.base.AnalysisMethod method) (pytransit.analysis.base.TransitGUIBase method) console_message_inplace() (pytransit.analysis.base.AnalysisMethod method) (pytransit.analysis.base.TransitGUIBase method) ConvertSelectFunc() (pytransit.transit_gui.TnSeekFrame method) convertToCombinedWig() (in module pytransit.transit_tools), [1] convertToGeneCountSummary() (in module pytransit.transit_tools), [1] convertToIGV() (in module pytransit.transit_tools), [1] cterm (pytransit.tnseq_tools.Genes attribute), [1] ctrlAll() (pytransit.transit_gui.TnSeekFrame method) ctrlRemoveFunc() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) ctrlSelected() (pytransit.transit_gui.TnSeekFrame method) ctrlToIGV() (pytransit.transit_gui.MainFrame method) ctrlViewFunc() (pytransit.transit_gui.TnSeekFrame method) cumulative_average() (in module pytransit.stat_tools), [1]

D

datasetSelectFunc() (pytransit.trash.TrashFrame method) dberndiff() (in module pytransit.stat_tools), [1] dbinomdiff() (in module pytransit.stat_tools), [1] defineCheckBox() (pytransit.analysis.base.AnalysisGUI method) defineChoiceBox() (pytransit.analysis.base.AnalysisGUI method) definePanel() (pytransit.analysis.base.AnalysisGUI method) (pytransit.analysis.binomial.BinomialGUI method) (pytransit.analysis.griffin.GriffinGUI method) (pytransit.analysis.gumbel.GumbelGUI method) (pytransit.analysis.hmm.HMMGUI method) (pytransit.analysis.rankproduct.RankProductGUI method) (pytransit.analysis.resampling.ResamplingGUI method) (pytransit.analysis.tn5gaps.Tn5GapsGUI method) defineTextBox() (pytransit.analysis.base.AnalysisGUI method) desc (pytransit.tnseq_tools.Gene attribute), [1]

dirname() (in module pytransit.transit_tools), [1] displayFileFunc() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) displayHistogram() (pytransit.analysis.resampling.ResamplingFile method) displayInTrackView() (pytransit.analysis.base.TransitFile method) documentationFunc() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) draw_canvas() (in module pytransit.draw_trash) draw_features() (in module pytransit.draw_trash) draw_genes() (in module pytransit.draw_trash) draw_reads() (in module pytransit.draw_trash) draw_scale() (in module pytransit.draw_trash) draw_ta_sites() (in module pytransit.draw_trash) DrawCanvas() (pytransit.trash.TrashFrame method) DualConditionMethod (class in pytransit.analysis.base)

E

ecdf() (in module pytransit.norm_tools), [1] (pytransit.norm_tools.AdaptiveBGCNorm method), [1] (pytransit.norm_tools.BetaGeomNorm method), [1] EmpHistNorm (class in pytransit.norm_tools), [1] empirical_theta() (in module pytransit.norm_tools), [1] (pytransit.norm_tools.TTRNorm method), [1] Enable() (pytransit.analysis.base.AnalysisGUI method) end (pytransit.tnseq_tools.Gene attribute), [1] ExampleAnalysis (class in pytransit.analysis.example) ExampleFile (class in pytransit.analysis.example) ExampleGUI (class in pytransit.analysis.example)

ExampleMethod (class in pytransit.analysis.example) Exit() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) expAll() (pytransit.transit_gui.TnSeekFrame method) ExpectedRuns() (in module pytransit.tnseq_tools), [1] ExpectedRuns_cached() (pytransit.analysis.gumbel.GumbelMethod method) ExportSelectFunc() (pytransit.transit_gui.TnSeekFrame method) expRemoveFunc() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) expSelected() (pytransit.transit_gui.TnSeekFrame method) expToIGV() (pytransit.transit_gui.MainFrame method) expViewFunc() (pytransit.transit_gui.TnSeekFrame method)

F

F_mean_diff_dict() (in module pytransit.stat_tools), [1] F_mean_diff_flat() (in module pytransit.stat_tools), [1] F_non() (pytransit.analysis.gumbel.GumbelMethod method) F_shuffle_dict_libraries() (in module pytransit.stat_tools), [1] F_shuffle_flat() (in module pytransit.stat_tools), [1] F_sum_diff_dict() (in module pytransit.stat_tools), [1] F_sum_diff_flat() (in module pytransit.stat_tools), [1] fact() (in module pytransit.stat_tools), [1] fetch_name() (in module pytransit.transit_tools), [1] (in module pytransit.trash) fileActionFunc() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) fileSelected() (pytransit.transit_gui.TnSeekFrame method) filter_wigs_by_conditions() (pytransit.analysis.base.MultiConditionMethod method) (pytransit.analysis.resampling.ResamplingMethod method) filter_wigs_by_conditions2() (pytransit.analysis.base.MultiConditionMethod method) filter_wigs_by_conditions3() (pytransit.analysis.base.MultiConditionMethod method) filterMethodsByTransposon() (pytransit.transit_gui.TnSeekFrame method) finish() (pytransit.analysis.base.AnalysisMethod method) finishRun() (pytransit.transit_gui.TnSeekFrame method) forward_procedure() (pytransit.analysis.hmm.HMMMethod method) fromargs() (pytransit.analysis.anova.AnovaMethod class method) (pytransit.analysis.base.AnalysisMethod class method) (pytransit.analysis.binomial.BinomialMethod class method) (pytransit.analysis.example.ExampleMethod class method) (pytransit.analysis.griffin.GriffinMethod class method) (pytransit.analysis.gumbel.GumbelMethod class method) (pytransit.analysis.hmm.HMMMethod class method) (pytransit.analysis.rankproduct.RankProductMethod class method) (pytransit.analysis.resampling.ResamplingMethod class method) (pytransit.analysis.tn5gaps.Tn5GapsMethod class method)

fromconsole() (pytransit.analysis.base.AnalysisMethod class method) fromGUI() (pytransit.analysis.base.AnalysisMethod class method) (pytransit.analysis.binomial.BinomialMethod class method) (pytransit.analysis.example.ExampleMethod class method) (pytransit.analysis.griffin.GriffinMethod class method) (pytransit.analysis.gumbel.GumbelMethod class method) (pytransit.analysis.hmm.HMMMethod class method) (pytransit.analysis.rankproduct.RankProductMethod class method) (pytransit.analysis.resampling.ResamplingMethod class method) (pytransit.analysis.tn5gaps.Tn5GapsMethod class method) fullname() (pytransit.analysis.base.TransitAnalysis method) FWER_Bayes() (in module pytransit.stat_tools), [1] Fzinfnb() (in module pytransit.norm_tools), [1] (pytransit.norm_tools.EmpHistNorm static method), [1]

G

Gene (class in pytransit.tnseq_tools), [1] Genes (class in pytransit.tnseq_tools), [1] genes (pytransit.tnseq_tools.Genes attribute), [1] get_coordinate_map() (in module pytransit.tnseq_tools), [1] get_data() (in module pytransit.tnseq_tools), [1] get_data_stats() (in module pytransit.tnseq_tools), [1] get_data_w_genome() (in module pytransit.tnseq_tools), [1] get_data_zero_fill() (in module pytransit.tnseq_tools), [1] get_dynamic_height() (in module pytransit.draw_trash) get_extended_pos_hash() (in module pytransit.transit_tools), [1] get_extended_pos_hash_gff() (in module pytransit.tnseq_tools), [1] get_extended_pos_hash_pt() (in module pytransit.tnseq_tools), [1] get_file_types() (in module pytransit.tnseq_tools), [1] get_gap_span() (pytransit.tnseq_tools.Gene method), [1] get_gene_info() (in module pytransit.tnseq_tools), [1] (in module pytransit.transit_tools), [1] get_gene_info_gff() (in module pytransit.tnseq_tools), [1] get_gene_info_pt() (in module pytransit.tnseq_tools), [1] get_gene_span() (pytransit.tnseq_tools.Gene method), [1] get_genes_in_range() (in module pytransit.tnseq_tools), [1] get_lib_data_dict() (in module pytransit.stat_tools), [1] get_pos_hash() (in module pytransit.tnseq_tools), [1] (in module pytransit.transit_tools), [1] get_pos_hash_gff() (in module pytransit.tnseq_tools), [1] get_pos_hash_pt() (in module pytransit.tnseq_tools), [1] get_samples_metadata() (pytransit.analysis.base.MultiConditionMethod method) get_unknown_file_types() (in module pytransit.tnseq_tools), [1] get_validated_data() (in module pytransit.transit_tools), [1] get_wig_stats() (in module pytransit.tnseq_tools), [1] GetColLabelValue() (pytransit.fileDisplay.TransitTable method) getData() (pytransit.analysis.base.TransitFile method) getDescriptionText() (pytransit.analysis.base.TransitAnalysis method) getE1() (in module pytransit.tnseq_tools), [1] getE2() (in module pytransit.tnseq_tools), [1] getGamma() (in module pytransit.tnseq_tools), [1] getHeader() (pytransit.analysis.base.TransitFile method) (pytransit.analysis.binomial.BinomialFile method) (pytransit.analysis.example.ExampleFile method) (pytransit.analysis.griffin.GriffinFile method) (pytransit.analysis.gumbel.GumbelFile method) (pytransit.analysis.hmm.HMMGenesFile method) (pytransit.analysis.hmm.HMMSitesFile method) (pytransit.analysis.resampling.ResamplingFile method) (pytransit.analysis.tn5gaps.Tn5GapsFile method)

getHMMHash() (pytransit.trash.TrashFrame method) getInfoFromFileType() (in module pytransit.fileDisplay) getInstructionsText() (pytransit.analysis.base.TransitAnalysis method) getMenus() (pytransit.analysis.base.TransitFile method) (pytransit.analysis.resampling.ResamplingFile method) GetNumberCols() (pytransit.fileDisplay.TransitTable method) GetNumberRows() (pytransit.fileDisplay.TransitTable method) getR1() (in module pytransit.tnseq_tools), [1] getR2() (in module pytransit.tnseq_tools), [1] GetRawValue() (pytransit.fileDisplay.TransitTable method) GetRowLabelValue() (pytransit.fileDisplay.TransitTable method) getTabTableData() (in module pytransit.transit_tools), [1] getTransposonsText() (pytransit.analysis.base.TransitAnalysis method) GetValue() (pytransit.fileDisplay.TransitTable method) global_insertion() (pytransit.tnseq_tools.Genes method), [1] global_phi() (pytransit.tnseq_tools.Genes method), [1] global_reads() (pytransit.tnseq_tools.Genes method), [1] global_run() (pytransit.tnseq_tools.Genes method), [1] global_sites() (pytransit.tnseq_tools.Genes method), [1] global_theta() (pytransit.tnseq_tools.Genes method), [1] GlobalDisable() (pytransit.analysis.base.AnalysisGUI method) (pytransit.analysis.resampling.ResamplingGUI method) GlobalEnable() (pytransit.analysis.base.AnalysisGUI method) (pytransit.analysis.resampling.ResamplingGUI method) GlobalHide() (pytransit.analysis.base.AnalysisGUI method) GlobalShow() (pytransit.analysis.base.AnalysisGUI method) good_orf() (pytransit.analysis.gumbel.GumbelMethod method) graphGeneCounts() (pytransit.transit_gui.TnSeekFrame method) graphRankedZbar() (pytransit.transit_gui.TnSeekFrame method) graphVolcanoPlot() (pytransit.transit_gui.TnSeekFrame method) griffin_analysis() (in module pytransit.tnseq_tools), [1] GriffinAnalysis (class in pytransit.analysis.griffin) GriffinFile (class in pytransit.analysis.griffin) GriffinGUI (class in pytransit.analysis.griffin) GriffinMethod (class in pytransit.analysis.griffin) group_by_condition() (pytransit.analysis.anova.AnovaMethod method) GumbelAnalysis (class in pytransit.analysis.gumbel) GumbelCDF() (in module pytransit.tnseq_tools), [1] GumbelFile (class in pytransit.analysis.gumbel) GumbelGUI (class in pytransit.analysis.gumbel) GumbelMethod (class in pytransit.analysis.gumbel)

H

HDI_from_MCMC() (in module pytransit.stat_tools), [1] Hide() (pytransit.analysis.base.AnalysisGUI method) HideAllOptions() (pytransit.transit_gui.TnSeekFrame method) HideGlobalCTerminus() (pytransit.transit_gui.TnSeekFrame method) HideGlobalCtrlLibraries() (pytransit.transit_gui.TnSeekFrame method) HideGlobalExpLibraries() (pytransit.transit_gui.TnSeekFrame method) HideGlobalLibraries() (pytransit.transit_gui.TnSeekFrame method)

HideGlobalNTerminus() (pytransit.transit_gui.TnSeekFrame method) HideGlobalOptions() (pytransit.transit_gui.TnSeekFrame method) HideProgressSection() (pytransit.transit_gui.TnSeekFrame method) HMMAnalysis (class in pytransit.analysis.hmm) HMMGenesFile (class in pytransit.analysis.hmm) HMMGUI (class in pytransit.analysis.hmm) HMMMethod (class in pytransit.analysis.hmm) HMMSitesFile (class in pytransit.analysis.hmm)

I

ignoreCodon (pytransit.tnseq_tools.Genes attribute), [1] ImgFrame (class in pytransit.fileDisplay) include_nc (pytransit.tnseq_tools.Genes attribute), [1]

InfoIcon (class in pytransit.analysis.base) intersect_size() (pytransit.analysis.tn5gaps.Tn5GapsMethod method) InvalidArgumentException isEven() (in module pytransit.stat_tools), [1]

L

leftFunc() (pytransit.trash.TrashFrame method) (pytransit.view_trash.MainFrame method) loadCtrlFile() (pytransit.transit_gui.TnSeekFrame method) loadCtrlFileFunc() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) loadExpFile() (pytransit.transit_gui.TnSeekFrame method) loadExpFileFunc() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) local_gap_span() (pytransit.tnseq_tools.Genes method), [1] local_gene_span() (pytransit.tnseq_tools.Genes method), [1] local_insertions() (pytransit.tnseq_tools.Genes method), [1]

local_phis() (pytransit.tnseq_tools.Genes method), [1] local_reads() (pytransit.tnseq_tools.Genes method), [1] local_runs() (pytransit.tnseq_tools.Genes method), [1] local_sites() (pytransit.tnseq_tools.Genes method), [1] local_thetas() (pytransit.tnseq_tools.Genes method), [1] loess() (in module pytransit.stat_tools), [1] loess_correction() (in module pytransit.stat_tools), [1] LoessPrevFunc() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) log_fac() (in module pytransit.stat_tools), [1] loglik() (in module pytransit.stat_tools), [1]

M

main() (in module pytransit.analysis.anova) MainFrame (class in pytransit.transit_gui) (class in pytransit.view_trash) maxrun() (in module pytransit.tnseq_tools), [1] means_by_condition_for_gene() (pytransit.analysis.anova.AnovaMethod method) means_by_rv() (pytransit.analysis.anova.AnovaMethod method) MethodSelectFunc() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) minread (pytransit.tnseq_tools.Genes attribute), [1] module pytransit, [1] pytransit.analysis pytransit.analysis.anova pytransit.analysis.base pytransit.analysis.binomial pytransit.analysis.example pytransit.analysis.griffin pytransit.analysis.gumbel pytransit.analysis.hmm pytransit.analysis.rankproduct pytransit.analysis.resampling pytransit.analysis.tn5gaps pytransit.draw_trash pytransit.fileDisplay pytransit.images pytransit.norm_tools, [1] pytransit.qcDisplay pytransit.stat_tools, [1] pytransit.tnseq_tools, [1] pytransit.transit_gui pytransit.transit_tools, [1] pytransit.trash pytransit.view_trash

MultiConditionMethod (class in pytransit.analysis.base) multinomial() (in module pytransit.stat_tools), [1] my_perm() (in module pytransit.stat_tools), [1]

N

name (pytransit.norm_tools.AdaptiveBGCNorm attribute), [1] (pytransit.norm_tools.BetaGeomNorm attribute), [1] (pytransit.norm_tools.EmpHistNorm attribute), [1] (pytransit.norm_tools.NoNorm attribute), [1] (pytransit.norm_tools.NormMethod attribute), [1] (pytransit.norm_tools.NZMeanNorm attribute), [1] (pytransit.norm_tools.QuantileNorm attribute), [1] (pytransit.norm_tools.TotReadsNorm attribute), [1] (pytransit.norm_tools.TTRNorm attribute), [1] (pytransit.norm_tools.ZeroInflatedNBNorm attribute), [1] (pytransit.tnseq_tools.Gene attribute), [1] NoNorm (class in pytransit.norm_tools), [1] norm (pytransit.tnseq_tools.Genes attribute), [1] norm() (in module pytransit.stat_tools), [1] norm_to_target() (in module pytransit.norm_tools), [1]

normalize() (in module pytransit.draw_trash) (pytransit.norm_tools.AdaptiveBGCNorm static method), [1] (pytransit.norm_tools.BetaGeomNorm static method), [1] (pytransit.norm_tools.EmpHistNorm static method), [1] (pytransit.norm_tools.NoNorm static method), [1] (pytransit.norm_tools.NormMethod static method), [1] (pytransit.norm_tools.NZMeanNorm static method), [1] (pytransit.norm_tools.QuantileNorm static method), [1] (pytransit.norm_tools.TotReadsNorm static method), [1] (pytransit.norm_tools.TTRNorm static method), [1] (pytransit.norm_tools.ZeroInflatedNBNorm static method), [1] normalize_data() (in module pytransit.norm_tools), [1] NormMethod (class in pytransit.norm_tools), [1] nterm (pytransit.tnseq_tools.Genes attribute), [1] NZMeanNorm (class in pytransit.norm_tools), [1]

O

OnCellRightClicked() (pytransit.fileDisplay.TransitGridFrame method) OnClose() (pytransit.qcDisplay.qcFrame method) (pytransit.transit_gui.AssumeZerosDialog method) (pytransit.transit_tools.AssumeZerosDialog method), [1] onHimar1Checked() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) OnLabelDoubleClicked() (pytransit.fileDisplay.TransitGridFrame method)

onNormSelect() (pytransit.qcDisplay.qcFrame method) onStatsItemSelect() (pytransit.qcDisplay.qcFrame method) onTn5Checked() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) OpenFile() (pytransit.transit_gui.TnSeekFrame method) (pytransit.trash.TrashFrame method) orf (pytransit.tnseq_tools.Gene attribute), [1] orf2index (pytransit.tnseq_tools.Genes attribute), [1]

P

parse_lib_index() (in module pytransit.stat_tools), [1] parseCoords() (in module pytransit.transit_tools), [1] phi() (pytransit.tnseq_tools.Gene method), [1] phi_coefficient() (in module pytransit.stat_tools), [1] PilImageToWxBitmap() (in module pytransit.qcDisplay) (in module pytransit.trash) PilImageToWxImage() (in module pytransit.qcDisplay) (in module pytransit.trash) position (pytransit.tnseq_tools.Gene attribute), [1] post_process_genes() (pytransit.analysis.hmm.HMMMethod method) preprocess_data() (pytransit.analysis.resampling.ResamplingMethod method) print_members() (pytransit.analysis.base.AnalysisMethod method) progress_range() (pytransit.analysis.base.AnalysisMethod method) progress_update() (pytransit.analysis.base.AnalysisMethod method) protTable (pytransit.tnseq_tools.Genes attribute), [1] pytransit module, [1] pytransit.analysis module pytransit.analysis.anova module pytransit.analysis.base module pytransit.analysis.binomial module pytransit.analysis.example module pytransit.analysis.griffin module pytransit.analysis.gumbel module

pytransit.analysis.hmm module pytransit.analysis.rankproduct module pytransit.analysis.resampling module pytransit.analysis.tn5gaps module pytransit.draw_trash module pytransit.fileDisplay module pytransit.images module pytransit.norm_tools module, [1] pytransit.qcDisplay module pytransit.stat_tools module, [1] pytransit.tnseq_tools module, [1] pytransit.transit_gui module pytransit.transit_tools module, [1] pytransit.trash module pytransit.view_trash module

Q

qberndiff() (in module pytransit.stat_tools), [1] qbinomdiff() (in module pytransit.stat_tools), [1] qcFrame (class in pytransit.qcDisplay)

qcFunc() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) QuadConditionMethod (class in pytransit.analysis.base) QuantileNorm (class in pytransit.norm_tools), [1]

R

RankProductAnalysis (class in pytransit.analysis.rankproduct) RankProductFile (class in pytransit.analysis.rankproduct) RankProductGUI (class in pytransit.analysis.rankproduct) RankProductMethod (class in pytransit.analysis.rankproduct) read_combined_wig() (in module pytransit.tnseq_tools), [1] read_genes() (in module pytransit.tnseq_tools), [1] read_genome() (in module pytransit.tnseq_tools), [1] read_samples_metadata() (in module pytransit.tnseq_tools), [1] reads (pytransit.tnseq_tools.Gene attribute), [1] refresh() (pytransit.qcDisplay.qcFrame method) refreshPlots() (pytransit.qcDisplay.qcFrame method) regress() (in module pytransit.stat_tools), [1] reps (pytransit.tnseq_tools.Genes attribute), [1] resampling() (in module pytransit.stat_tools), [1] ResamplingAnalysis (class in pytransit.analysis.resampling) ResamplingFile (class in pytransit.analysis.resampling) ResamplingGUI (class in pytransit.analysis.resampling) ResamplingMethod (class in pytransit.analysis.resampling) resetFunc() (pytransit.trash.TrashFrame method) (pytransit.view_trash.MainFrame method) ResetProgress() (pytransit.transit_gui.TnSeekFrame method) rightFunc() (pytransit.trash.TrashFrame method) (pytransit.view_trash.MainFrame method)

Run() (pytransit.analysis.anova.AnovaMethod method) (pytransit.analysis.base.AnalysisMethod method) (pytransit.analysis.binomial.BinomialMethod method) (pytransit.analysis.example.ExampleMethod method) (pytransit.analysis.griffin.GriffinMethod method) (pytransit.analysis.gumbel.GumbelMethod method) (pytransit.analysis.hmm.HMMMethod method) (pytransit.analysis.rankproduct.RankProductMethod method) (pytransit.analysis.resampling.ResamplingMethod method) (pytransit.analysis.tn5gaps.Tn5GapsMethod method) run_anova() (pytransit.analysis.anova.AnovaMethod method) run_resampling() (pytransit.analysis.resampling.ResamplingMethod method) RunBinomialFunc() (pytransit.transit_gui.MainFrame method) RunDEHMMFunc() (pytransit.transit_gui.MainFrame method) RunHMMFunc() (pytransit.transit_gui.MainFrame method) runindex() (in module pytransit.tnseq_tools), [1] RunMethod() (pytransit.transit_gui.TnSeekFrame method) RunResamplingFunc() (pytransit.transit_gui.MainFrame method) runs() (in module pytransit.tnseq_tools), [1] runs_w_info() (in module pytransit.tnseq_tools), [1] rv_siteindexes_map() (in module pytransit.tnseq_tools), [1]

S

sample_trunc_norm_post() (in module pytransit.stat_tools), [1] sample_Z() (pytransit.analysis.gumbel.GumbelMethod method) SaveFile() (pytransit.transit_gui.TnSeekFrame method) (pytransit.trash.TrashFrame method) saveHistogram() (pytransit.transit_gui.TnSeekFrame method) saveImageFunc() (pytransit.trash.TrashFrame method) (pytransit.view_trash.MainFrame method) scaleFunc() (pytransit.trash.TrashFrame method) scatterFunc() (pytransit.transit_gui.MainFrame method) (pytransit.transit_gui.TnSeekFrame method) searchFunc() (pytransit.trash.TrashFrame method) (pytransit.view_trash.MainFrame method) select_conditions() (pytransit.analysis.base.MultiConditionMethod method) setProgressRange() (pytransit.transit_gui.TnSeekFrame method) SetValue() (pytransit.fileDisplay.TransitTable method) Show() (pytransit.analysis.base.AnalysisGUI method) ShowAskWarning() (in module pytransit.transit_tools), [1]

ShowError() (in module pytransit.transit_tools), [1] ShowGlobalCTerminus() (pytransit.transit_gui.TnSeekFrame method) ShowGlobalCtrlLibraries() (pytransit.transit_gui.TnSeekFrame method) ShowGlobalExpLibraries() (pytransit.transit_gui.TnSeekFrame method) ShowGlobalLibraries() (pytransit.transit_gui.TnSeekFrame method) ShowGlobalNTerminus() (pytransit.transit_gui.TnSeekFrame method) ShowGlobalOptions() (pytransit.transit_gui.TnSeekFrame method) ShowMessage() (in module pytransit.transit_tools), [1] ShowProgressSection() (pytransit.transit_gui.TnSeekFrame method) sigmoid() (pytransit.analysis.gumbel.GumbelMethod method) SingleConditionMethod (class in pytransit.analysis.base) SortableListCtrl (class in pytransit.fileDisplay) SortColumn() (pytransit.fileDisplay.TransitTable method) start (pytransit.tnseq_tools.Gene attribute), [1] statsSelected() (pytransit.qcDisplay.qcFrame method) status_message() (pytransit.analysis.base.AnalysisMethod method) (pytransit.analysis.base.TransitGUIBase method) strand (pytransit.tnseq_tools.Gene attribute), [1]

T

text_histogram() (in module pytransit.stat_tools), [1] theta() (pytransit.tnseq_tools.Gene method), [1] Tn5GapsAnalysis (class in pytransit.analysis.tn5gaps) Tn5GapsFile (class in pytransit.analysis.tn5gaps) Tn5GapsGUI (class in pytransit.analysis.tn5gaps) Tn5GapsMethod (class in pytransit.analysis.tn5gaps) TnSeekFrame (class in pytransit.transit_gui) tosses() (pytransit.tnseq_tools.Genes method), [1] tossify() (in module pytransit.tnseq_tools), [1] total_reads() (pytransit.tnseq_tools.Gene method), [1] (pytransit.tnseq_tools.Genes method), [1] TotReadsNorm (class in pytransit.norm_tools), [1] track_message() (pytransit.trash.TrashFrame method) transformToRange() (in module pytransit.stat_tools), [1] transit_error() (in module pytransit.transit_tools), [1] (pytransit.analysis.anova.AnovaMethod class method) (pytransit.analysis.base.AnalysisMethod method) (pytransit.analysis.base.TransitGUIBase method)

transit_message() (in module pytransit.transit_tools), [1] (pytransit.analysis.base.AnalysisMethod method) (pytransit.analysis.base.TransitGUIBase method) transit_message_inplace() (pytransit.analysis.base.AnalysisMethod method) (pytransit.analysis.base.TransitGUIBase method) transit_warning() (pytransit.analysis.base.AnalysisMethod method) (pytransit.analysis.base.TransitGUIBase method) TransitAnalysis (class in pytransit.analysis.base) TransitFile (class in pytransit.analysis.base) TransitGridFrame (class in pytransit.fileDisplay) TransitGUIBase (class in pytransit.analysis.base) TransitTable (class in pytransit.fileDisplay) TrashFrame (class in pytransit.trash) tricoeff() (in module pytransit.stat_tools), [1] tricube() (in module pytransit.stat_tools), [1] trimmed_empirical_mu() (in module pytransit.norm_tools), [1] (pytransit.norm_tools.TTRNorm method), [1] TTRNorm (class in pytransit.norm_tools), [1]

U

unknownColNames() (in module pytransit.fileDisplay) unknownFileHeaderText() (in module pytransit.fileDisplay) unknownTableData() (in module pytransit.fileDisplay) updateFiles() (pytransit.qcDisplay.qcFrame method) updateFunc() (pytransit.trash.TrashFrame method) (pytransit.view_trash.MainFrame method) updateGraphChoices() (pytransit.transit_gui.TnSeekFrame method) updateProgress() (pytransit.transit_gui.TnSeekFrame method) updateStatus() (pytransit.transit_gui.TnSeekFrame method)

usage_string() (pytransit.analysis.anova.AnovaMethod class method) (pytransit.analysis.base.AnalysisMethod class method) (pytransit.analysis.binomial.BinomialMethod class method) (pytransit.analysis.example.ExampleMethod class method) (pytransit.analysis.griffin.GriffinMethod class method) (pytransit.analysis.gumbel.GumbelMethod class method) (pytransit.analysis.hmm.HMMMethod class method) (pytransit.analysis.rankproduct.RankProductMethod class method) (pytransit.analysis.resampling.ResamplingMethod class method) (pytransit.analysis.tn5gaps.Tn5GapsMethod class method)

V

validate_annotation() (in module pytransit.transit_tools), [1] validate_both_datasets() (in module pytransit.transit_tools), [1] validate_control_datasets() (in module pytransit.transit_tools), [1] validate_filetypes() (in module pytransit.transit_tools), [1]

validate_transposons_used() (in module pytransit.transit_tools), [1] validate_wig_format() (in module pytransit.transit_tools), [1] VarR() (in module pytransit.tnseq_tools), [1] viterbi() (pytransit.analysis.hmm.HMMMethod method)

W

wigList (pytransit.tnseq_tools.Genes attribute), [1] wigs_to_conditions() (pytransit.analysis.anova.AnovaMethod method) (pytransit.analysis.resampling.ResamplingMethod method) winsorize() (pytransit.analysis.anova.AnovaMethod method) winsorize_resampling() (pytransit.analysis.resampling.ResamplingMethod method) write_output() (pytransit.analysis.resampling.ResamplingMethod method)

WxBitmapToPilImage() (in module pytransit.qcDisplay) (in module pytransit.trash) WxBitmapToWxImage() (in module pytransit.qcDisplay) (in module pytransit.trash) WxImageToWxBitmap() (in module pytransit.qcDisplay) (in module pytransit.trash)

Z

ZeroInflatedNBNorm (class in pytransit.norm_tools), [1] zinfnb_factors() (in module pytransit.norm_tools), [1] zoomInFunc() (pytransit.trash.TrashFrame method) (pytransit.view_trash.MainFrame method)

zoomOutFunc() (pytransit.trash.TrashFrame method) (pytransit.view_trash.MainFrame method)