TRANSIT
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TRANSIT Overview
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Running TRANSIT
Quality Control
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Console Mode Cheat-Sheet
TRANSIT Tutorials
Tutorial: Genetic Interactions Analysis
Tutorial: Normalize datasets
Tutorial: Export datasets
TPP Manual
TPP Overview
Installation
Running TPP
Mapping to Genomes with Multiple Contigs
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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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]
aton() (in module pytransit.transit_tools)
,
[1]
B
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]
boxcoxTable() (in module pytransit.stat_tools)
,
[1]
boxcoxtransform() (in module pytransit.stat_tools)
,
[1]
C
check_wig_includes_zeros() (in module pytransit.tnseq_tools)
,
[1]
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_lib_dicts() (in module pytransit.stat_tools)
,
[1]
combine_replicates() (in module pytransit.tnseq_tools)
,
[1]
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]
cumulative_average() (in module pytransit.stat_tools)
,
[1]
D
dberndiff() (in module pytransit.stat_tools)
,
[1]
dbinomdiff() (in module pytransit.stat_tools)
,
[1]
desc (pytransit.tnseq_tools.Gene attribute)
,
[1]
dirname() (in module pytransit.transit_tools)
,
[1]
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]
end (pytransit.tnseq_tools.Gene attribute)
,
[1]
ExpectedRuns() (in module pytransit.tnseq_tools)
,
[1]
F
F_mean_diff_dict() (in module pytransit.stat_tools)
,
[1]
F_mean_diff_flat() (in module pytransit.stat_tools)
,
[1]
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]
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_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_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]
getE1() (in module pytransit.tnseq_tools)
,
[1]
getE2() (in module pytransit.tnseq_tools)
,
[1]
getGamma() (in module pytransit.tnseq_tools)
,
[1]
getR1() (in module pytransit.tnseq_tools)
,
[1]
getR2() (in module pytransit.tnseq_tools)
,
[1]
getTabTableData() (in module pytransit.transit_tools)
,
[1]
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]
griffin_analysis() (in module pytransit.tnseq_tools)
,
[1]
GumbelCDF() (in module pytransit.tnseq_tools)
,
[1]
H
HDI_from_MCMC() (in module pytransit.stat_tools)
,
[1]
I
ignoreCodon (pytransit.tnseq_tools.Genes attribute)
,
[1]
include_nc (pytransit.tnseq_tools.Genes attribute)
,
[1]
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
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]
position (pytransit.tnseq_tools.Gene attribute)
,
[1]
protTable (pytransit.tnseq_tools.Genes attribute)
,
[1]
pytransit (module)
,
[1]
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
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]
regress() (in module pytransit.stat_tools)
,
[1]
reps (pytransit.tnseq_tools.Genes attribute)
,
[1]
resampling() (in module pytransit.stat_tools)
,
[1]
runindex() (in module pytransit.tnseq_tools)
,
[1]
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]
ShowAskWarning() (in module pytransit.transit_tools)
,
[1]
ShowError() (in module pytransit.transit_tools)
,
[1]
ShowMessage() (in module pytransit.transit_tools)
,
[1]
start (pytransit.tnseq_tools.Gene attribute)
,
[1]
strand (pytransit.tnseq_tools.Gene attribute)
,
[1]
T
text_histogram() (in module pytransit.stat_tools)
,
[1]
theta() (pytransit.tnseq_tools.Gene method)
,
[1]
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]
transit_message() (in module pytransit.transit_tools)
,
[1]
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]
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]
W
wigList (pytransit.tnseq_tools.Genes attribute)
,
[1]
Z
ZeroInflatedNBNorm (class in pytransit.norm_tools)
,
[1]
zinfnb_factors() (in module pytransit.norm_tools)
,
[1]
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