Name		Name	Last commit message	Last commit date
Latest commit History 115 Commits
mutation_clusters		mutation_clusters
BAF_second_filter.py		BAF_second_filter.py
CN_data_2expands_fm_results7.py		CN_data_2expands_fm_results7.py
Mary_data.py		Mary_data.py
Python program structure.pptx		Python program structure.pptx
README.md		README.md
SNP2Expands.py		SNP2Expands.py
SNPFilterFinder_bloodBEdiff.py		SNPFilterFinder_bloodBEdiff.py
analyze_expands_inpatient_congruence.py		analyze_expands_inpatient_congruence.py
assemble_ploidy_evidence.py		assemble_ploidy_evidence.py
branch_lengths_and_signature_calculator.py		branch_lengths_and_signature_calculator.py
calculate_diploid_likelihood.py		calculate_diploid_likelihood.py
calculate_joint_histograms.py		calculate_joint_histograms.py
calculate_joint_scatterplots.py		calculate_joint_scatterplots.py
calculate_kanika_odds.py		calculate_kanika_odds.py
calculate_odds.py		calculate_odds.py
calculate_position_histograms_by_length.py		calculate_position_histograms_by_length.py
calibrate_CN_histograms.py		calibrate_CN_histograms.py
calibrate_CN_values.py		calibrate_CN_values.py
check_95_ratio.py		check_95_ratio.py
check_expands_disjoint.py		check_expands_disjoint.py
check_expands_trees.py		check_expands_trees.py
check_unequal_cns.py		check_unequal_cns.py
check_xiaohong_cnloh.py		check_xiaohong_cnloh.py
check_xiaohong_distances.py		check_xiaohong_distances.py
choose_best_analysis.py		choose_best_analysis.py
cluster_VAFs.py		cluster_VAFs.py
cluster_VAFs_422.py		cluster_VAFs_422.py
cluster_VAFs_Mary.py		cluster_VAFs_Mary.py
collect_maxps.py		collect_maxps.py
collect_purity_ploidy.py		collect_purity_ploidy.py
collect_spstats_noise.py		collect_spstats_noise.py
compareXiaohongToAscat.py		compareXiaohongToAscat.py
compare_19578.py		compare_19578.py
compare_1M_probe_sets.py		compare_1M_probe_sets.py
compare_CN_estimates.py		compare_CN_estimates.py
compare_SV_groups_to_trees.py		compare_SV_groups_to_trees.py
compare_groups_and_trees.py		compare_groups_and_trees.py
compare_joint_segs.py		compare_joint_segs.py
compare_probe_sets.py		compare_probe_sets.py
convertXiaohongToEvents.py		convertXiaohongToEvents.py
count_ploidy_evidence.py		count_ploidy_evidence.py
count_shared_vs_VAF.py		count_shared_vs_VAF.py
create_ASCAT_histograms.py		create_ASCAT_histograms.py
create_BAF_segments_rejoined.py		create_BAF_segments_rejoined.py
create_BEAST_input.py		create_BEAST_input.py
create_CN-BAF_histograms.py		create_CN-BAF_histograms.py
create_CN-BAF_segments.py		create_CN-BAF_segments.py
create_combined_pASCAT_input.py		create_combined_pASCAT_input.py
create_delgains_from_BEAST.py		create_delgains_from_BEAST.py
create_diseq_histograms.py		create_diseq_histograms.py
create_expands_input.py		create_expands_input.py
create_full_expands_input.py		create_full_expands_input.py
create_joint_seg_file.py		create_joint_seg_file.py
create_new_BEAST_input.py		create_new_BEAST_input.py
create_pASCAT_input.py		create_pASCAT_input.py
create_ploidy_estimates_from_pASCAT.py		create_ploidy_estimates_from_pASCAT.py
create_rejoined_histograms.py		create_rejoined_histograms.py
create_seglength_histograms.py		create_seglength_histograms.py
distribute_BEAST.py		distribute_BEAST.py
estimate_gamma.py		estimate_gamma.py
exome2Expands.py		exome2Expands.py
extract_CN_from_Jabba.py		extract_CN_from_Jabba.py
findVAFHistogramPeaks.py		findVAFHistogramPeaks.py
find_SNP_groups.py		find_SNP_groups.py
find_VAF_peaks.py		find_VAF_peaks.py
find_deletions.py		find_deletions.py
find_dupes.py		find_dupes.py
find_example_loss.py		find_example_loss.py
find_example_loss_rejoined.py		find_example_loss_rejoined.py
find_p16.py		find_p16.py
four_gamete_persample.py		four_gamete_persample.py
four_gamete_test.py		four_gamete_test.py
full_segmentation_analysis.py		full_segmentation_analysis.py
full_segmentation_by_position_creator.py		full_segmentation_by_position_creator.py
full_segmentation_histogram_creator.py		full_segmentation_histogram_creator.py
getCNVs.py		getCNVs.py
getChromosomeCentromere.py		getChromosomeCentromere.py
get_noninteger_CN_from_ASCAT.py		get_noninteger_CN_from_ASCAT.py
hand_cluster_mutation_vecs.py		hand_cluster_mutation_vecs.py
highlownoisevals.py		highlownoisevals.py
lucianSNPLibrary.py		lucianSNPLibrary.py
makeBoxPlotForPatty.py		makeBoxPlotForPatty.py
make_VAF_histograms.py		make_VAF_histograms.py
make_gamma_test_sge_files.py		make_gamma_test_sge_files.py
make_overlap_probesets.py		make_overlap_probesets.py
make_overlap_three_probesets.py		make_overlap_three_probesets.py
make_pASCAT_sge_files.py		make_pASCAT_sge_files.py
make_phylip_levels_parsimony_input.py		make_phylip_levels_parsimony_input.py
make_phylip_parsimony_input.py		make_phylip_parsimony_input.py
make_phylip_seqboot_input.py		make_phylip_seqboot_input.py
make_run_thinned.py		make_run_thinned.py
make_shuffled_directories.py		make_shuffled_directories.py
makeround2.py		makeround2.py
mary_VAFHistogramPeaks.py		mary_VAFHistogramPeaks.py
median_calc.py		median_calc.py
new_cluster_VAFs.py		new_cluster_VAFs.py
new_mutation.py		new_mutation.py
output_teeth_stomach_statuses.py		output_teeth_stomach_statuses.py
p_rawsegs.py		p_rawsegs.py

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kuhner-python

Python programs written for the Kuhner lab

luciansmith/kuhner-python

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