TRANSIT
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TRANSIT Manual
Overview
Installation
Running TRANSIT
Features
Analysis Methods
Console Mode Cheat-Sheet
TRANSIT Tutorials
Tutorial: Essentiality Analysis in a Single Condition
Tutorial: Essentiality Analysis of the Entire Genome
Tutorial: Comparative Analysis - Glycerol vs Cholesterol
Tutorial: Normalize datasets
Tutorial: Export datasets
TPP Manual
Overview
Installation
Running TPP
Overview of Data Processing Procedure
Statistics
Code Documentation
transit package
TRANSIT
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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]
__eq__() (pytransit.tnseq_tools.Gene method)
,
[1]
__ge__() (pytransit.tnseq_tools.Gene method)
,
[1]
__getitem__() (pytransit.tnseq_tools.Gene method)
,
[1]
(pytransit.tnseq_tools.Genes method)
,
[1]
__gt__() (pytransit.tnseq_tools.Gene method)
,
[1]
__le__() (pytransit.tnseq_tools.Gene 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
AdaptiveBGCNorm (class in pytransit.norm_tools)
,
[1]
add_file() (pytransit.analysis.base.AnalysisMethod method)
AnalysisGUI (class in pytransit.analysis.base)
AnalysisMethod (class in pytransit.analysis.base)
aton() (in module pytransit.transit_tools)
,
[1]
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]
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)
calculate_pins() (pytransit.analysis.hmm.HMMMethod method)
check_wig_includes_zeros() (in module pytransit.tnseq_tools)
,
[1]
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]
comb() (in module pytransit.stat_tools)
,
[1]
comb1() (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)
convertToCombinedWig() (in module pytransit.transit_tools)
,
[1]
cterm (pytransit.tnseq_tools.Genes attribute)
,
[1]
cumulative_average() (in module pytransit.stat_tools)
,
[1]
D
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]
displayHistogram() (pytransit.analysis.resampling.ResamplingFile method)
displayInTrackView() (pytransit.analysis.base.TransitFile 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)
ExpectedRuns() (in module pytransit.tnseq_tools)
,
[1]
F
F_mean_diff_flat() (in module pytransit.stat_tools)
,
[1]
F_non() (pytransit.analysis.gumbel.GumbelMethod method)
F_shuffle_flat() (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]
finish() (pytransit.analysis.base.AnalysisMethod 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]
(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_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_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_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]
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)
getInstructionsText() (pytransit.analysis.base.TransitAnalysis method)
getMenus() (pytransit.analysis.base.TransitFile method)
(pytransit.analysis.resampling.ResamplingFile method)
getR1() (in module pytransit.tnseq_tools)
,
[1]
getR2() (in module pytransit.tnseq_tools)
,
[1]
getTabTableData() (in module pytransit.transit_tools)
,
[1]
getTransposonsText() (pytransit.analysis.base.TransitAnalysis 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]
good_orf() (pytransit.analysis.gumbel.GumbelMethod 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)
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
Hide() (pytransit.analysis.base.AnalysisGUI 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]
include_nc (pytransit.tnseq_tools.Genes attribute)
,
[1]
intersect_size() (pytransit.analysis.tn5gaps.Tn5GapsMethod method)
InvalidArgumentException
isEven() (in module pytransit.stat_tools)
,
[1]
L
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]
log_fac() (in module pytransit.stat_tools)
,
[1]
loglik() (in module pytransit.stat_tools)
,
[1]
M
maxrun() (in module pytransit.tnseq_tools)
,
[1]
minread (pytransit.tnseq_tools.Genes attribute)
,
[1]
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.NZMeanNorm attribute)
,
[1]
(pytransit.norm_tools.NoNorm attribute)
,
[1]
(pytransit.norm_tools.NormMethod attribute)
,
[1]
(pytransit.norm_tools.QuantileNorm attribute)
,
[1]
(pytransit.norm_tools.TTRNorm attribute)
,
[1]
(pytransit.norm_tools.TotReadsNorm 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() (pytransit.norm_tools.AdaptiveBGCNorm static method)
,
[1]
(pytransit.norm_tools.BetaGeomNorm static method)
,
[1]
(pytransit.norm_tools.EmpHistNorm static method)
,
[1]
(pytransit.norm_tools.NZMeanNorm static method)
,
[1]
(pytransit.norm_tools.NoNorm static method)
,
[1]
(pytransit.norm_tools.NormMethod static method)
,
[1]
(pytransit.norm_tools.QuantileNorm static method)
,
[1]
(pytransit.norm_tools.TTRNorm static method)
,
[1]
(pytransit.norm_tools.TotReadsNorm 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
orf (pytransit.tnseq_tools.Gene attribute)
,
[1]
orf2index (pytransit.tnseq_tools.Genes attribute)
,
[1]
P
parseCoords() (in module pytransit.transit_tools)
,
[1]
phi() (pytransit.tnseq_tools.Gene method)
,
[1]
phi_coefficient() (in module pytransit.stat_tools)
,
[1]
position (pytransit.tnseq_tools.Gene attribute)
,
[1]
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]
pytransit (module)
,
[1]
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.norm_tools (module)
,
[1]
pytransit.stat_tools (module)
,
[1]
pytransit.tnseq_tools (module)
,
[1]
pytransit.transit_tools (module)
,
[1]
Q
qberndiff() (in module pytransit.stat_tools)
,
[1]
qbinomdiff() (in module pytransit.stat_tools)
,
[1]
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_genome() (in module pytransit.tnseq_tools)
,
[1]
reads (pytransit.tnseq_tools.Gene attribute)
,
[1]
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)
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)
runindex() (in module pytransit.tnseq_tools)
,
[1]
runs() (in module pytransit.tnseq_tools)
,
[1]
runs_w_info() (in module pytransit.tnseq_tools)
,
[1]
S
sample_Z() (pytransit.analysis.gumbel.GumbelMethod method)
Show() (pytransit.analysis.base.AnalysisGUI method)
ShowAskWarning() (in module pytransit.transit_tools)
,
[1]
ShowError() (in module pytransit.transit_tools)
,
[1]
ShowMessage() (in module pytransit.transit_tools)
,
[1]
sigmoid() (pytransit.analysis.gumbel.GumbelMethod method)
SingleConditionMethod (class in pytransit.analysis.base)
start (pytransit.tnseq_tools.Gene attribute)
,
[1]
status_message() (pytransit.analysis.base.AnalysisMethod method)
(pytransit.analysis.base.TransitGUIBase method)
strand (pytransit.tnseq_tools.Gene attribute)
,
[1]
T
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)
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]
transformToRange() (in module pytransit.stat_tools)
,
[1]
transit_error() (in module pytransit.transit_tools)
,
[1]
(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)
TransitGUIBase (class in pytransit.analysis.base)
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
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]
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]
Z
ZeroInflatedNBNorm (class in pytransit.norm_tools)
,
[1]
zinfnb_factors() (in module pytransit.norm_tools)
,
[1]
Read the Docs
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Versions
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