GitHub - wrshoemaker/microbiome_evolution: Scripts for analyzing evolutionary dynamics in large cohorts of human gut metagenomes

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Scripts for analyzing evolutionary dynamics in large cohorts of human gut metagenomes

BSD-2-Clause license

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Name		Name	Last commit message	Last commit date
Latest commit History 396 Commits
bash_scripts		bash_scripts
error_filtering_cpp_code		error_filtering_cpp_code
old_code		old_code
old_scripts		old_scripts
qsub_scripts		qsub_scripts
H12_H2H1_MIDAS.py		H12_H2H1_MIDAS.py
HMP1-2_ids_order.txt		HMP1-2_ids_order.txt
HMP_ids.txt		HMP_ids.txt
HMP_ids_order.txt		HMP_ids_order.txt
HMP_phenotypes.txt		HMP_phenotypes.txt
LICENSE		LICENSE
README		README
analyze_simulations_species_abundance.py		analyze_simulations_species_abundance.py
calculate_all_substitution_rates.py		calculate_all_substitution_rates.py
calculate_all_temporal_changes.py		calculate_all_temporal_changes.py
calculate_coverage_distribution.py		calculate_coverage_distribution.py
calculate_error_pvalues.py		calculate_error_pvalues.py
calculate_linkage_disequilibria.py		calculate_linkage_disequilibria.py
calculate_linkage_disequilibria_simulations.py		calculate_linkage_disequilibria_simulations.py
calculate_marker_coverage_distribution.py		calculate_marker_coverage_distribution.py
calculate_marker_gene_coverage.py		calculate_marker_gene_coverage.py
calculate_preexisting_snps.py		calculate_preexisting_snps.py
calculate_private_snvs.py		calculate_private_snvs.py
calculate_singletons.py		calculate_singletons.py
calculate_snp_errors.py		calculate_snp_errors.py
calculate_snp_prevalences.py		calculate_snp_prevalences.py
calculate_snv_distances.py		calculate_snv_distances.py
calculate_substitution_rates.py		calculate_substitution_rates.py
calculate_temporal_changes.py		calculate_temporal_changes.py
calculate_within_person_sfs.py		calculate_within_person_sfs.py
clade_utils.py		clade_utils.py
combine_replicates.py		combine_replicates.py
concatenate_Li_2016_FMT_fastq.py		concatenate_Li_2016_FMT_fastq.py
concatenate_fastq_sample_replicates_from_same_visno.py		concatenate_fastq_sample_replicates_from_same_visno.py
concatenate_fastq_technical_replicates.py		concatenate_fastq_technical_replicates.py
config (Benjamin’s iMac's conflicted copy 2018-08-24).py		config (Benjamin’s iMac's conflicted copy 2018-08-24).py
config.py		config.py
core_gene_utils.py		core_gene_utils.py
count_reads_per_ref_genome.py		count_reads_per_ref_genome.py
create_clade_definition_table.py		create_clade_definition_table.py
create_genome_features_file.py		create_genome_features_file.py
diversity_utils.py		diversity_utils.py
documentation.txt		documentation.txt
error_filtering.py		error_filtering.py
fastq_samples_without_visno_replicate.py		fastq_samples_without_visno_replicate.py
figure_utils.py		figure_utils.py
find_orthologs.py		find_orthologs.py
find_orthologs_multispecies.py		find_orthologs_multispecies.py
gene_changes_annotation.py		gene_changes_annotation.py
gene_changes_annotation_cross_species.py		gene_changes_annotation_cross_species.py
gene_differences_kegg_annotations.py		gene_differences_kegg_annotations.py
gene_differences_reference_genome_change.py		gene_differences_reference_genome_change.py
gene_diversity_utils.py		gene_diversity_utils.py
gene_filter_output.txt		gene_filter_output.txt
generate_all_figures.py		generate_all_figures.py
get_list_of_subject_ids.py		get_list_of_subject_ids.py
isolates_genome_list.txt		isolates_genome_list.txt
korpela_twin_ids.txt		korpela_twin_ids.txt
kuleshov_ids.txt		kuleshov_ids.txt
list_of_relevant_patric_files.py		list_of_relevant_patric_files.py
loop_over_species_wrapper.py		loop_over_species_wrapper.py
loop_over_technical_replicates.py		loop_over_technical_replicates.py
manual_clade_definitions.txt		manual_clade_definitions.txt
midas_db_utils.py		midas_db_utils.py
mixture_labels.txt		mixture_labels.txt
parse_HMP_data.py		parse_HMP_data.py
parse_HMP_metadata.py		parse_HMP_metadata.py
parse_marker_genes_blast_output.py		parse_marker_genes_blast_output.py
parse_midas_data.py		parse_midas_data.py
parse_patric.py		parse_patric.py
parse_simulated_data.py		parse_simulated_data.py
pipe_midas_data.py		pipe_midas_data.py
plot_coverage_distribution.py		plot_coverage_distribution.py
plot_cumulative_abundance_curves.py		plot_cumulative_abundance_curves.py
plot_diploid_sweeps.py		plot_diploid_sweeps.py
plot_doubleton_distribution.py		plot_doubleton_distribution.py
plot_doubleton_singleton_ratios.py		plot_doubleton_singleton_ratios.py
plot_figure_1.py		plot_figure_1.py
plot_figure_2.py		plot_figure_2.py
plot_figure_2_simulations.py		plot_figure_2_simulations.py
plot_figure_3.py		plot_figure_3.py
plot_figure_3_simulations.py		plot_figure_3_simulations.py
plot_figure_3_thinned.py		plot_figure_3_thinned.py
plot_figure_3a.py		plot_figure_3a.py
plot_figure_3b.py		plot_figure_3b.py
plot_figure_4 (Benjamin’s iMac's conflicted copy 2018-09-11).py		plot_figure_4 (Benjamin’s iMac's conflicted copy 2018-09-11).py
plot_figure_4.py		plot_figure_4.py
plot_figure_4_simulations.py		plot_figure_4_simulations.py
plot_figure_4_simulations_3panels.py		plot_figure_4_simulations_3panels.py
plot_figure_5.py		plot_figure_5.py
plot_figure_5_simulations.py		plot_figure_5_simulations.py
plot_figure_6.py		plot_figure_6.py
plot_figure_6.py.071318.py		plot_figure_6.py.071318.py
plot_figure_7.py		plot_figure_7.py
plot_figure_for_katy.py		plot_figure_for_katy.py
plot_fragilis_figure_6.py		plot_fragilis_figure_6.py
plot_gene_copynum_distribution.py		plot_gene_copynum_distribution.py
plot_gene_differences_vs_pi.py		plot_gene_differences_vs_pi.py
plot_gene_haplotypes.py		plot_gene_haplotypes.py
plot_gene_ld_condition_freq.py		plot_gene_ld_condition_freq.py

Repository files navigation

This project provides associated computer code for the manuscript:

NR Garud*, BH Good*, O Hallatschek, and KS Pollard. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLoS Biol 17(1): e3000102 (2019).