Index
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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I
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L
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M
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O
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P
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R
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S
C
calculate_and_plot_DNV_heatmap() (isomut2py.mutationcalling.MutationCaller method)
calculate_and_plot_DNV_spectrum() (isomut2py.mutationcalling.MutationCaller method)
calculate_and_plot_indel_spectrum() (isomut2py.mutationcalling.MutationCaller method)
calculate_and_plot_SNV_spectrum() (isomut2py.mutationcalling.MutationCaller method)
calculate_DNV_matrix() (in module isomut2py.postprocess)
(isomut2py.mutationcalling.MutationCaller method)
calculate_DNV_spectrum() (in module isomut2py.postprocess)
(isomut2py.mutationcalling.MutationCaller method)
calculate_indel_spectrum() (in module isomut2py.postprocess)
(isomut2py.mutationcalling.MutationCaller method)
calculate_SNV_spectrum() (in module isomut2py.postprocess)
(isomut2py.mutationcalling.MutationCaller method)
check_interval_for_difference() (in module isomut2py.compare)
check_pileup() (in module isomut2py.postprocess)
(isomut2py.mutationcalling.MutationCaller method)
compare_with_bed() (in module isomut2py.compare)
compare_with_other() (isomut2py.ploidyestimation.PloidyEstimator method)
compare_with_other_PloidyEstimator() (in module isomut2py.compare)
D
decompose_DNV_spectra() (in module isomut2py.postprocess)
(isomut2py.mutationcalling.MutationCaller method)
decompose_indel_spectra() (in module isomut2py.postprocess)
(isomut2py.mutationcalling.MutationCaller method)
decompose_SNV_spectra() (in module isomut2py.postprocess)
(isomut2py.mutationcalling.MutationCaller method)
double_run() (in module isomut2py.process)
download_example_data() (in module isomut2py.examples)
download_raw_example_data() (in module isomut2py.examples)
E
estimate_hapcov_infmix() (in module isomut2py.bayesian)
(isomut2py.ploidyestimation.PloidyEstimator method)
F
fit_gaussians() (in module isomut2py.bayesian)
(isomut2py.ploidyestimation.PloidyEstimator method)
G
generate_HTML_report_for_ploidy_est() (in module isomut2py.plot)
(isomut2py.ploidyestimation.PloidyEstimator method)
generate_ploidy_info_file() (in module isomut2py.format)
get_bed_format_for_sample() (in module isomut2py.format)
(isomut2py.ploidyestimation.PloidyEstimator method)
get_coverage_distribution() (in module isomut2py.io)
(isomut2py.ploidyestimation.PloidyEstimator method)
get_details_for_mutations() (in module isomut2py.postprocess)
(isomut2py.mutationcalling.MutationCaller method)
I
isomut2py.bayesian (module)
isomut2py.compare (module)
isomut2py.examples (module)
isomut2py.format (module)
isomut2py.io (module)
isomut2py.mutationcalling (module)
isomut2py.ploidyestimation (module)
isomut2py.plot (module)
isomut2py.postprocess (module)
isomut2py.process (module)
L
load_bedfile_from_file() (in module isomut2py.io)
(isomut2py.ploidyestimation.PloidyEstimator method)
load_cov_distribution_parameters_from_file() (in module isomut2py.io)
(isomut2py.ploidyestimation.PloidyEstimator method)
load_example_mutdet_settings() (in module isomut2py.examples)
load_example_ploidyest_settings() (in module isomut2py.examples)
load_mutations() (in module isomut2py.io)
(isomut2py.mutationcalling.MutationCaller method)
load_obj() (in module isomut2py.io)
load_preprocessed_example_ploidyest_settings() (in module isomut2py.examples)
M
MutationCaller (class in isomut2py.mutationcalling)
O
optimize_results() (in module isomut2py.postprocess)
(isomut2py.mutationcalling.MutationCaller method)
optimize_score() (in module isomut2py.postprocess)
P
PE_on_chrom() (in module isomut2py.bayesian)
(isomut2py.ploidyestimation.PloidyEstimator method)
PE_on_range() (in module isomut2py.bayesian)
PE_on_whole_genome() (isomut2py.ploidyestimation.PloidyEstimator method)
PE_prepare_temp_files() (in module isomut2py.process)
PloidyEstimator (class in isomut2py.ploidyestimation)
plot_coverage_distribution() (in module isomut2py.plot)
(isomut2py.ploidyestimation.PloidyEstimator method)
plot_DNV_heatmap() (in module isomut2py.plot)
(isomut2py.mutationcalling.MutationCaller method)
plot_DNV_spectrum() (in module isomut2py.plot)
(isomut2py.mutationcalling.MutationCaller method)
plot_hierarchical_clustering() (in module isomut2py.plot)
(isomut2py.mutationcalling.MutationCaller method)
plot_indel_spectrum() (in module isomut2py.plot)
(isomut2py.mutationcalling.MutationCaller method)
plot_karyotype_for_all_chroms() (in module isomut2py.plot)
(isomut2py.ploidyestimation.PloidyEstimator method)
plot_karyotype_for_chrom() (in module isomut2py.plot)
plot_karyotype_summary() (in module isomut2py.plot)
(isomut2py.ploidyestimation.PloidyEstimator method)
plot_mutation_counts() (in module isomut2py.plot)
(isomut2py.mutationcalling.MutationCaller method)
plot_rainfall() (in module isomut2py.plot)
(isomut2py.mutationcalling.MutationCaller method)
plot_SNV_spectrum() (in module isomut2py.plot)
(isomut2py.mutationcalling.MutationCaller method)
R
run_isomut2_mutdet() (isomut2py.mutationcalling.MutationCaller method)
run_ploidy_estimation() (isomut2py.ploidyestimation.PloidyEstimator method)
S
save_obj() (in module isomut2py.io)
single_run() (in module isomut2py.process)
isomut2py
Comprehensive detection and analysis of genomic mutations from NGS sequencing data
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Importing external mutations
Advanced ploidy estimation
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