TRANSIT
v2.0.0
TRANSIT Manual
Overview
Installation
Running TRANSIT
Analysis Methods
TRANSIT Tutorials
Tutorial: Essentiality Analysis in a Single Condition
Tutorial: Essentiality Analysis of the Entire Genome
Tutorial: Comparative Analysis - Glycerol vs Cholesterol
Tutorial: Export datasets
TPP Manual
Overview
Installation
Running TPP
Overview of Data Processing Procedure
Statistics
Code Documentation
transit package
TRANSIT
Docs
»
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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Z
_
__contains__() (pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
__eq__() (pytransit.tnseq_tools.Gene method)
,
[1]
,
[2]
__ge__() (pytransit.tnseq_tools.Gene method)
,
[1]
,
[2]
__getitem__() (pytransit.tnseq_tools.Gene method)
,
[1]
,
[2]
(pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
__gt__() (pytransit.tnseq_tools.Gene method)
,
[1]
,
[2]
__le__() (pytransit.tnseq_tools.Gene method)
,
[1]
,
[2]
__len__() (pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
__lt__() (pytransit.tnseq_tools.Gene method)
,
[1]
,
[2]
__str__() (pytransit.tnseq_tools.Gene method)
,
[1]
,
[2]
(pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
A
aBGC_norm() (in module pytransit.norm_tools)
,
[1]
,
[2]
aboutFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
add_file() (pytransit.analysis.base.AnalysisMethod method)
addFeatureFunc() (pytransit.trash.TrashFrame method)
,
[1]
(pytransit.view_trash.MainFrame method)
,
[1]
addFile() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
addFileFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
addFiles() (pytransit.qcDisplay.qcFrame method)
,
[1]
addPlots() (pytransit.qcDisplay.qcFrame method)
,
[1]
allSelected() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
allViewFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
AnalysisGUI (class in pytransit.analysis.base)
AnalysisMethod (class in pytransit.analysis.base)
annotationFileFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
annotationGFF3_to_PT() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
annotationPT_to_GFF3() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
annotationPT_to_PTT() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
annotationPTT_to_PT() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
aton() (in module pytransit.transit_tools)
,
[1]
,
[2]
AutoResizeCols() (pytransit.fileDisplay.TransitGridFrame method)
,
[1]
B
backward_procedure() (pytransit.analysis.hmm.HMMMethod method)
basename() (in module pytransit.transit_tools)
,
[1]
,
[2]
bayesian_ess_thresholds() (in module pytransit.stat_tools)
,
[1]
,
[2]
betageom_norm() (in module pytransit.norm_tools)
,
[1]
,
[2]
BH_fdr_correction() (in module pytransit.stat_tools)
,
[1]
,
[2]
binom() (in module pytransit.stat_tools)
,
[1]
,
[2]
binom_cdf() (in module pytransit.stat_tools)
,
[1]
,
[2]
binom_test() (in module pytransit.stat_tools)
,
[1]
,
[2]
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]
,
[2]
boxcoxtransform() (in module pytransit.stat_tools)
,
[1]
,
[2]
C
calc_overlap() (pytransit.analysis.tn5gaps.Tn5GapsMethod method)
calculate_pins() (pytransit.analysis.hmm.HMMMethod method)
chooseNormalization() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
choseMethodsMenu() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
classify() (pytransit.analysis.gumbel.GumbelMethod method)
cleanargs() (in module pytransit.transit_tools)
,
[1]
,
[2]
cleaninfgeom() (in module pytransit.norm_tools)
,
[1]
,
[2]
comb() (in module pytransit.stat_tools)
,
[1]
,
[2]
comb1() (in module pytransit.stat_tools)
,
[1]
,
[2]
combine_replicates() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
console_message() (pytransit.analysis.base.AnalysisMethod method)
console_message_inplace() (pytransit.analysis.base.AnalysisMethod method)
convertToCombinedWig() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
convertToCombinedWigGUI() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
convertToIGV() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
convertToIGVGUI() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
cterm (pytransit.tnseq_tools.Genes attribute)
,
[1]
,
[2]
ctrlAll() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
ctrlRemoveFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
ctrlSelected() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
ctrlToIGV() (pytransit.transit_gui.MainFrame method)
,
[1]
ctrlViewFunc() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
D
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)
desc (pytransit.tnseq_tools.Gene attribute)
,
[1]
,
[2]
displayFileFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
displayHistogram() (pytransit.analysis.resampling.ResamplingFile method)
displayInTrackView() (pytransit.analysis.base.TransitFile method)
documentationFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
draw_canvas() (in module pytransit.draw_trash)
,
[1]
draw_features() (in module pytransit.draw_trash)
,
[1]
draw_genes() (in module pytransit.draw_trash)
,
[1]
draw_reads() (in module pytransit.draw_trash)
,
[1]
draw_scale() (in module pytransit.draw_trash)
,
[1]
draw_ta_sites() (in module pytransit.draw_trash)
,
[1]
DualConditionMethod (class in pytransit.analysis.base)
E
ecdf() (in module pytransit.norm_tools)
,
[1]
,
[2]
emphist_factors() (in module pytransit.norm_tools)
,
[1]
,
[2]
empirical_theta() (in module pytransit.norm_tools)
,
[1]
,
[2]
Enable() (pytransit.analysis.base.AnalysisGUI method)
end (pytransit.tnseq_tools.Gene attribute)
,
[1]
,
[2]
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)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
expAll() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
ExpectedRuns() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
expRemoveFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
expSelected() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
expToIGV() (pytransit.transit_gui.MainFrame method)
,
[1]
expViewFunc() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
F
F_mean_diff_flat() (in module pytransit.stat_tools)
,
[1]
,
[2]
F_non() (pytransit.analysis.gumbel.GumbelMethod method)
F_shuffle_flat() (in module pytransit.stat_tools)
,
[1]
,
[2]
F_sum_diff_flat() (in module pytransit.stat_tools)
,
[1]
,
[2]
fact() (in module pytransit.stat_tools)
,
[1]
,
[2]
fetch_name() (in module pytransit.fileDisplay)
,
[1]
(in module pytransit.transit_tools)
,
[1]
,
[2]
(in module pytransit.trash)
,
[1]
fileActionFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
fileSelected() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
filterMethodsByTransposon() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
finish() (pytransit.analysis.base.AnalysisMethod method)
finishRun() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
forward_procedure() (pytransit.analysis.hmm.HMMMethod method)
fromargs() (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)
Fzinfnb() (in module pytransit.norm_tools)
,
[1]
,
[2]
G
Gene (class in pytransit.tnseq_tools)
,
[1]
,
[2]
Genes (class in pytransit.tnseq_tools)
,
[1]
,
[2]
genes (pytransit.tnseq_tools.Genes attribute)
,
[1]
,
[2]
get_coordinate_map() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
get_data() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
get_data_zero_fill() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
get_dynamic_height() (in module pytransit.draw_trash)
,
[1]
get_file_types() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
get_gap_span() (pytransit.tnseq_tools.Gene method)
,
[1]
,
[2]
get_gene_info() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
get_gene_span() (pytransit.tnseq_tools.Gene method)
,
[1]
,
[2]
get_genes_in_range() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
get_pos_hash() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
get_unknown_file_types() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
get_wig_stats() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
GetColLabelValue() (pytransit.fileDisplay.TransitTable method)
,
[1]
getData() (pytransit.analysis.base.TransitFile method)
getDescriptionText() (pytransit.analysis.base.TransitAnalysis method)
getE1() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
getE2() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
getGamma() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
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)
getInfoFromFileType() (in module pytransit.fileDisplay)
,
[1]
getInstructionsText() (pytransit.analysis.base.TransitAnalysis method)
getMenus() (pytransit.analysis.base.TransitFile method)
(pytransit.analysis.resampling.ResamplingFile method)
GetNumberCols() (pytransit.fileDisplay.TransitTable method)
,
[1]
GetNumberRows() (pytransit.fileDisplay.TransitTable method)
,
[1]
getR1() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
getR2() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
GetRawValue() (pytransit.fileDisplay.TransitTable method)
,
[1]
GetRowLabelValue() (pytransit.fileDisplay.TransitTable method)
,
[1]
getTabTableData() (in module pytransit.transit_tools)
,
[1]
,
[2]
getTransposonsText() (pytransit.analysis.base.TransitAnalysis method)
GetValue() (pytransit.fileDisplay.TransitTable method)
,
[1]
global_insertion() (pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
global_phi() (pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
global_reads() (pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
global_run() (pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
global_sites() (pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
global_theta() (pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
good_orf() (pytransit.analysis.gumbel.GumbelMethod method)
graphGeneCounts() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
graphRankedZbar() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
graphVolcanoPlot() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
griffin_analysis() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
GriffinAnalysis (class in pytransit.analysis.griffin)
GriffinFile (class in pytransit.analysis.griffin)
GriffinGUI (class in pytransit.analysis.griffin)
GriffinMethod (class in pytransit.analysis.griffin)
GumbelAnalysis (class in pytransit.analysis.gumbel)
GumbelCDF() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
GumbelFile (class in pytransit.analysis.gumbel)
GumbelGUI (class in pytransit.analysis.gumbel)
GumbelMethod (class in pytransit.analysis.gumbel)
H
hash_prot_genes() (in module pytransit.draw_trash)
,
[1]
Hide() (pytransit.analysis.base.AnalysisGUI method)
HideAllOptions() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
HideGlobalOptions() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
HideProgressSection() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.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]
,
[2]
ImgFrame (class in pytransit.fileDisplay)
,
[1]
include_nc (pytransit.tnseq_tools.Genes attribute)
,
[1]
,
[2]
intersect_size() (pytransit.analysis.tn5gaps.Tn5GapsMethod method)
L
leftFunc() (pytransit.trash.TrashFrame method)
,
[1]
(pytransit.view_trash.MainFrame method)
,
[1]
loadCtrlFileFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
loadExpFileFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
local_gap_span() (pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
local_gene_span() (pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
local_insertions() (pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
local_phis() (pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
local_reads() (pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
local_runs() (pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
local_sites() (pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
local_thetas() (pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
loess() (in module pytransit.stat_tools)
,
[1]
,
[2]
loess_correction() (in module pytransit.stat_tools)
,
[1]
,
[2]
LoessPrevFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
loglik() (in module pytransit.stat_tools)
,
[1]
,
[2]
M
MainFrame (class in pytransit.transit_gui)
,
[1]
(class in pytransit.view_trash)
,
[1]
maxrun() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
MethodSelectFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
minread (pytransit.tnseq_tools.Genes attribute)
,
[1]
,
[2]
msg() (in module runtransit)
MyFrame2 (class in view_qc)
N
name (pytransit.tnseq_tools.Gene attribute)
,
[1]
,
[2]
norm (pytransit.tnseq_tools.Genes attribute)
,
[1]
,
[2]
norm() (in module pytransit.stat_tools)
,
[1]
,
[2]
norm_to_target() (in module pytransit.norm_tools)
,
[1]
,
[2]
normalize() (in module pytransit.draw_trash)
,
[1]
normalize_data() (in module pytransit.norm_tools)
,
[1]
,
[2]
nterm (pytransit.tnseq_tools.Genes attribute)
,
[1]
,
[2]
nzmean_factors() (in module pytransit.norm_tools)
,
[1]
,
[2]
O
OnCellRightClicked() (pytransit.fileDisplay.TransitGridFrame method)
,
[1]
onHimar1Checked() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
OnLabelDoubleClicked() (pytransit.fileDisplay.TransitGridFrame method)
,
[1]
onStatsItemSelect() (pytransit.qcDisplay.qcFrame method)
,
[1]
onTn5Checked() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
OpenFile() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
orf (pytransit.tnseq_tools.Gene attribute)
,
[1]
,
[2]
orf2index (pytransit.tnseq_tools.Genes attribute)
,
[1]
,
[2]
P
parseCoords() (in module pytransit.transit_tools)
,
[1]
,
[2]
phi() (pytransit.tnseq_tools.Gene method)
,
[1]
,
[2]
phi_coefficient() (in module pytransit.stat_tools)
,
[1]
,
[2]
PilImageToWxBitmap() (in module pytransit.qcDisplay)
,
[1]
(in module pytransit.trash)
,
[1]
PilImageToWxImage() (in module pytransit.qcDisplay)
,
[1]
(in module pytransit.trash)
,
[1]
position (pytransit.tnseq_tools.Gene attribute)
,
[1]
,
[2]
post_process_genes() (pytransit.analysis.hmm.HMMMethod 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]
,
[2]
pytransit (module)
,
[1]
pytransit.__init__ (module)
pytransit.analysis (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)
,
[1]
pytransit.fileDisplay (module)
,
[1]
pytransit.images (module)
,
[1]
pytransit.norm_tools (module)
,
[1]
,
[2]
pytransit.qcDisplay (module)
,
[1]
pytransit.stat_tools (module)
,
[1]
,
[2]
pytransit.tnseq_tools (module)
,
[1]
,
[2]
pytransit.transit_gui (module)
,
[1]
pytransit.transit_tools (module)
,
[1]
,
[2]
pytransit.trash (module)
,
[1]
pytransit.view_trash (module)
,
[1]
Q
qcFrame (class in pytransit.qcDisplay)
,
[1]
qcFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
quantile_norm() (in module pytransit.norm_tools)
,
[1]
,
[2]
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_genome() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
read_prot_table() (in module pytransit.draw_trash)
,
[1]
reads (pytransit.tnseq_tools.Gene attribute)
,
[1]
,
[2]
regress() (in module pytransit.stat_tools)
,
[1]
,
[2]
reps (pytransit.tnseq_tools.Genes attribute)
,
[1]
,
[2]
resampling() (in module pytransit.stat_tools)
,
[1]
,
[2]
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)
,
[1]
(pytransit.view_trash.MainFrame method)
,
[1]
ResetProgress() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
rightFunc() (pytransit.trash.TrashFrame method)
,
[1]
(pytransit.view_trash.MainFrame method)
,
[1]
Run() (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)
RunBinomialFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
RunDEHMMFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
RunHMMFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
runindex() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
RunMethod() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
RunResamplingFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
runs() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
runs_w_info() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
runtransit (module)
S
sample_Z() (pytransit.analysis.gumbel.GumbelMethod method)
SaveFile() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(pytransit.trash.TrashFrame method)
,
[1]
(runtransit.TnSeekFrame method)
saveHistogram() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
saveImageFunc() (pytransit.trash.TrashFrame method)
,
[1]
(pytransit.view_trash.MainFrame method)
,
[1]
scatterFunc() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
searchFunc() (pytransit.trash.TrashFrame method)
,
[1]
(pytransit.view_trash.MainFrame method)
,
[1]
selectedToCombinedWig() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
selectedToIGV() (pytransit.transit_gui.MainFrame method)
,
[1]
(pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
setProgressRange() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
SetValue() (pytransit.fileDisplay.TransitTable method)
,
[1]
Show() (pytransit.analysis.base.AnalysisGUI method)
ShowAskWarning() (in module pytransit.transit_tools)
,
[1]
,
[2]
ShowError() (in module pytransit.fileDisplay)
,
[1]
(in module pytransit.transit_tools)
,
[1]
,
[2]
ShowGlobalOptions() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
ShowMessage() (in module pytransit.transit_tools)
,
[1]
,
[2]
ShowProgressSection() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
sigmoid() (pytransit.analysis.gumbel.GumbelMethod method)
SingleConditionMethod (class in pytransit.analysis.base)
SortableListCtrl (class in pytransit.fileDisplay)
,
[1]
sortColumn() (in module pytransit.fileDisplay)
,
[1]
SortColumn() (pytransit.fileDisplay.TransitTable method)
,
[1]
start (pytransit.tnseq_tools.Gene attribute)
,
[1]
,
[2]
statsSelected() (pytransit.qcDisplay.qcFrame method)
,
[1]
status_message() (pytransit.analysis.base.AnalysisMethod method)
strand (pytransit.tnseq_tools.Gene attribute)
,
[1]
,
[2]
T
test() (view_qc.MyFrame2 method)
theta() (pytransit.tnseq_tools.Gene method)
,
[1]
,
[2]
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)
,
[1]
(class in runtransit)
tosses() (pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
tossify() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
total_reads() (pytransit.tnseq_tools.Gene method)
,
[1]
,
[2]
(pytransit.tnseq_tools.Genes method)
,
[1]
,
[2]
totreads_factors() (in module pytransit.norm_tools)
,
[1]
,
[2]
transformToRange() (in module pytransit.stat_tools)
,
[1]
,
[2]
transit_error() (in module pytransit.transit_tools)
,
[1]
,
[2]
(pytransit.analysis.base.AnalysisMethod method)
transit_message() (in module pytransit.transit_tools)
,
[1]
,
[2]
(pytransit.analysis.base.AnalysisMethod method)
transit_message_inplace() (pytransit.analysis.base.AnalysisMethod method)
transit_warning() (pytransit.analysis.base.AnalysisMethod method)
TransitAnalysis (class in pytransit.analysis.base)
TransitFile (class in pytransit.analysis.base)
TransitGridFrame (class in pytransit.fileDisplay)
,
[1]
TransitTable (class in pytransit.fileDisplay)
,
[1]
TrashFrame (class in pytransit.trash)
,
[1]
tricube() (in module pytransit.stat_tools)
,
[1]
,
[2]
trimmed_empirical_mu() (in module pytransit.norm_tools)
,
[1]
,
[2]
TTR_factors() (in module pytransit.norm_tools)
,
[1]
,
[2]
U
unknownColNames() (in module pytransit.fileDisplay)
,
[1]
unknownFileHeaderText() (in module pytransit.fileDisplay)
,
[1]
unknownTableData() (in module pytransit.fileDisplay)
,
[1]
updateFunc() (pytransit.trash.TrashFrame method)
,
[1]
(pytransit.view_trash.MainFrame method)
,
[1]
updateGraphChoices() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
updateProgress() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
updateStatus() (pytransit.transit_gui.TnSeekFrame method)
,
[1]
(runtransit.TnSeekFrame method)
usage_string() (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]
,
[2]
validate_both_datasets() (in module pytransit.transit_tools)
,
[1]
,
[2]
validate_control_datasets() (in module pytransit.transit_tools)
,
[1]
,
[2]
validate_filetypes() (in module pytransit.transit_tools)
,
[1]
,
[2]
VarR() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
view_qc (module)
viterbi() (pytransit.analysis.hmm.HMMMethod method)
W
wigList (pytransit.tnseq_tools.Genes attribute)
,
[1]
,
[2]
WxBitmapToPilImage() (in module pytransit.qcDisplay)
,
[1]
(in module pytransit.trash)
,
[1]
WxBitmapToWxImage() (in module pytransit.qcDisplay)
,
[1]
(in module pytransit.trash)
,
[1]
WxImageToWxBitmap() (in module pytransit.qcDisplay)
,
[1]
(in module pytransit.trash)
,
[1]
Z
zinfnb_factors() (in module pytransit.norm_tools)
,
[1]
,
[2]
zoomInFunc() (pytransit.trash.TrashFrame method)
,
[1]
(pytransit.view_trash.MainFrame method)
,
[1]
zoomOutFunc() (pytransit.trash.TrashFrame method)
,
[1]
(pytransit.view_trash.MainFrame method)
,
[1]