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Contents:
Introduction
Installation
Citation
The
liquorice
python package
The LIQUORICE command-line-tool
LIQUORICE’s summary tool
Usage, Parameters, and Examples
LIQUORICE
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Index
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Index
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B
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C
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F
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G
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I
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L
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M
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N
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P
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R
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S
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Z
A
add_biasfactors_percentile_split() (in module liquorice.utils.Workflows)
aggregate_across_regions() (in module liquorice.utils.AggregateAcrossRegions)
B
BiasFactorHandler (class in liquorice.utils.BinTableBiasFactors)
BiasModel (class in liquorice.utils.BiasModel)
boxplot_score_summary() (in module liquorice.LIQUORICE_summary)
C
check_difference_to_control() (in module liquorice.LIQUORICE_summary)
correct_coverage_per_bin_for_cnas() (in module liquorice.utils.CorrectForCNAs)
CoverageAndSequenceTablePreparation (class in liquorice.utils.CoverageAndSequenceTablePreparation)
create_summary_table_LIQUORICE() (in module liquorice.LIQUORICE_summary)
F
filter_regions() (liquorice.utils.RegionFilteringAndBinning.RegionFilteringAndBinning method)
fit() (liquorice.utils.BiasModel.SklearnStyleRegressor method)
fit_gaussian_models() (liquorice.utils.FitGaussians.FitGaussians method)
FitGaussians (class in liquorice.utils.FitGaussians)
FullPaths (class in liquorice.LIQUORICE)
G
get_binsize_and_extendto_from_saved_settings() (in module liquorice.LIQUORICE_summary)
get_binstarts() (liquorice.utils.RegionFilteringAndBinning.RegionFilteringAndBinning method)
get_binstarts_percentile_split_central_roi() (liquorice.utils.RegionFilteringAndBinning.RegionFilteringAndBinning method)
get_CNV_corrected_coverage_for_bin() (in module liquorice.utils.CorrectForCNAs)
get_complete_table() (liquorice.utils.CoverageAndSequenceTablePreparation.CoverageAndSequenceTablePreparation method)
get_coverage_per_bin() (liquorice.utils.CoverageAndSequenceTablePreparation.CoverageAndSequenceTablePreparation method)
get_coverage_per_bin_mean_over_per_basepair_values_chunked() (liquorice.utils.CoverageAndSequenceTablePreparation.CoverageAndSequenceTablePreparation method)
get_dinuc_weights_binwide() (in module liquorice.utils.BiasFactorWeights)
get_fwd_mappability_bias_factor() (liquorice.utils.BinTableBiasFactors.BiasFactorHandler method)
get_GC_and_di_and_trinuc_weights() (liquorice.utils.BinTableBiasFactors.BiasFactorHandler method)
get_GC_bias_factor() (liquorice.utils.BinTableBiasFactors.BiasFactorHandler method)
get_GC_weights_binsize1() (in module liquorice.utils.BiasFactorWeights)
get_GC_weights_binwide() (in module liquorice.utils.BiasFactorWeights)
get_list_of_coveragefiles() (in module liquorice.LIQUORICE_summary)
get_list_of_fragment_lengths_and_avg_readlength() (in module liquorice.utils.GlobalFragmentSize)
get_mapp_weights_binwide() (in module liquorice.utils.BiasFactorWeights)
get_mappability_for_bin() (liquorice.utils.CoverageAndSequenceTablePreparation.CoverageAndSequenceTablePreparation method)
get_mappability_per_bin() (liquorice.utils.CoverageAndSequenceTablePreparation.CoverageAndSequenceTablePreparation method)
get_nucleotide_dicts() (in module liquorice.utils.BiasFactorWeights)
get_prediction_interval() (in module liquorice.LIQUORICE_summary)
get_prediction_interval_per_row() (in module liquorice.LIQUORICE_summary)
get_read_and_fragment_length() (in module liquorice.utils.GlobalFragmentSize)
get_rev_mappability_bias_factor() (liquorice.utils.BinTableBiasFactors.BiasFactorHandler method)
get_sequence_per_bin() (liquorice.utils.CoverageAndSequenceTablePreparation.CoverageAndSequenceTablePreparation method)
get_table_with_bias_factors() (liquorice.utils.BinTableBiasFactors.BiasFactorHandler method)
get_table_with_corrected_coverage_using_trained_biasmodel() (liquorice.utils.BiasModel.BiasModel method)
get_trinuc_weights_binwide() (in module liquorice.utils.BiasFactorWeights)
get_ymin_ymax_over_all_samples() (in module liquorice.LIQUORICE_summary)
getFragmentLength_worker() (in module liquorice.utils.GlobalFragmentSize)
getFragmentLength_wrapper() (in module liquorice.utils.GlobalFragmentSize)
I
is_within_chromsome_borders() (liquorice.utils.RegionFilteringAndBinning.RegionFilteringAndBinning method)
L
liquorice.LIQUORICE
module
liquorice.LIQUORICE_summary
module
liquorice.utils.AggregateAcrossRegions
module
liquorice.utils.BiasFactorWeights
module
liquorice.utils.BiasModel
module
liquorice.utils.BinTableBiasFactors
module
liquorice.utils.CorrectForCNAs
module
liquorice.utils.CoverageAndSequenceTablePreparation
module
liquorice.utils.FitGaussians
module
liquorice.utils.GlobalFragmentSize
module
liquorice.utils.MeanSequencingDepth
module
liquorice.utils.Plotting
module
liquorice.utils.RegionFilteringAndBinning
module
liquorice.utils.Workflows
module
M
main() (in module liquorice.LIQUORICE)
(in module liquorice.LIQUORICE_summary)
module
liquorice.LIQUORICE
liquorice.LIQUORICE_summary
liquorice.utils.AggregateAcrossRegions
liquorice.utils.BiasFactorWeights
liquorice.utils.BiasModel
liquorice.utils.BinTableBiasFactors
liquorice.utils.CorrectForCNAs
liquorice.utils.CoverageAndSequenceTablePreparation
liquorice.utils.FitGaussians
liquorice.utils.GlobalFragmentSize
liquorice.utils.MeanSequencingDepth
liquorice.utils.Plotting
liquorice.utils.RegionFilteringAndBinning
liquorice.utils.Workflows
N
none_or_list_of_float (liquorice.utils.Plotting.Plotting attribute)
none_or_list_of_int (liquorice.utils.Plotting.Plotting attribute)
none_or_list_of_str (liquorice.utils.Plotting.Plotting attribute)
P
parallelize_get_coverage_of_region() (in module liquorice.utils.CoverageAndSequenceTablePreparation)
parse_args() (in module liquorice.LIQUORICE)
(in module liquorice.LIQUORICE_summary)
plot_as_subplots() (in module liquorice.LIQUORICE_summary)
plot_control_distributions_and_test_normality() (in module liquorice.LIQUORICE_summary)
plot_corrected_vs_uncorrected_coverage() (liquorice.utils.Plotting.Plotting method)
plot_correlations_biasfactors_coverage_bin_nr() (liquorice.utils.Plotting.Plotting method)
plot_coverage_bias_correlation() (liquorice.utils.Plotting.Plotting method)
plot_fitted_model() (liquorice.utils.Plotting.Plotting method)
plot_overlay() (in module liquorice.LIQUORICE_summary)
Plotting (class in liquorice.utils.Plotting)
polyfit() (in module liquorice.utils.Plotting)
predict() (liquorice.utils.BiasModel.SklearnStyleRegressor method)
R
read_bed() (liquorice.utils.CoverageAndSequenceTablePreparation.CoverageAndSequenceTablePreparation method)
RegionFilteringAndBinning (class in liquorice.utils.RegionFilteringAndBinning)
run_get_coverage_of_region_per_chunk() (in module liquorice.utils.CoverageAndSequenceTablePreparation)
run_liquorice_on_regionset_with_pretrained_biasmodel() (in module liquorice.utils.Workflows)
run_liquorice_train_biasmodel_on_same_regions() (in module liquorice.utils.Workflows)
S
sample_bam_to_get_sequencing_depth() (in module liquorice.utils.MeanSequencingDepth)
score() (liquorice.utils.BiasModel.SklearnStyleRegressor method)
set_params() (liquorice.utils.BiasModel.SklearnStyleRegressor method)
SklearnStyleRegressor (class in liquorice.utils.BiasModel)
T
train_biasmodel() (liquorice.utils.BiasModel.BiasModel method)
train_biasmodel_2fold_CV_and_predict() (liquorice.utils.BiasModel.BiasModel method)
train_biasmodel_for_sample() (in module liquorice.utils.Workflows)
V
verify_consistant_binning_settings() (in module liquorice.LIQUORICE_summary)
W
write_bin_bedfile() (liquorice.utils.RegionFilteringAndBinning.RegionFilteringAndBinning method)
write_bin_bedfile_percentile_split_central_roi() (liquorice.utils.RegionFilteringAndBinning.RegionFilteringAndBinning method)
Z
zscore_to_control() (in module liquorice.LIQUORICE_summary)
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