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
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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]
,
[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]
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]
,
[2]
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)
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)
cterm (pytransit.tnseq_tools.Genes attribute)
,
[1]
,
[2]
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]
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]
,
[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)
ExpectedRuns() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
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.transit_tools)
,
[1]
,
[2]
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]
,
[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_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]
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)
getInstructionsText() (pytransit.analysis.base.TransitAnalysis method)
getMenus() (pytransit.analysis.base.TransitFile method)
(pytransit.analysis.resampling.ResamplingFile method)
getR1() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
getR2() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
getTabTableData() (in module pytransit.transit_tools)
,
[1]
,
[2]
getTransposonsText() (pytransit.analysis.base.TransitAnalysis method)
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)
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
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]
,
[2]
include_nc (pytransit.tnseq_tools.Genes attribute)
,
[1]
,
[2]
intersect_size() (pytransit.analysis.tn5gaps.Tn5GapsMethod method)
L
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]
loglik() (in module pytransit.stat_tools)
,
[1]
,
[2]
M
maxrun() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
minread (pytransit.tnseq_tools.Genes attribute)
,
[1]
,
[2]
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_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
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]
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.norm_tools (module)
,
[1]
,
[2]
pytransit.stat_tools (module)
,
[1]
,
[2]
pytransit.tnseq_tools (module)
,
[1]
,
[2]
pytransit.transit_tools (module)
,
[1]
,
[2]
Q
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]
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)
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]
,
[2]
runs() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
runs_w_info() (in module pytransit.tnseq_tools)
,
[1]
,
[2]
S
sample_Z() (pytransit.analysis.gumbel.GumbelMethod method)
Show() (pytransit.analysis.base.AnalysisGUI method)
ShowAskWarning() (in module pytransit.transit_tools)
,
[1]
,
[2]
ShowError() (in module pytransit.transit_tools)
,
[1]
,
[2]
ShowMessage() (in module pytransit.transit_tools)
,
[1]
,
[2]
sigmoid() (pytransit.analysis.gumbel.GumbelMethod method)
SingleConditionMethod (class in pytransit.analysis.base)
start (pytransit.tnseq_tools.Gene attribute)
,
[1]
,
[2]
status_message() (pytransit.analysis.base.AnalysisMethod method)
strand (pytransit.tnseq_tools.Gene attribute)
,
[1]
,
[2]
T
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)
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)
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
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]
viterbi() (pytransit.analysis.hmm.HMMMethod method)
W
wigList (pytransit.tnseq_tools.Genes attribute)
,
[1]
,
[2]
Z
zinfnb_factors() (in module pytransit.norm_tools)
,
[1]
,
[2]
Read the Docs
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