GitHub - mhyleung/public_transit_air_metagenomics: Input files and in-house scripts for public transit air microbiome and resistome manuscrirpt.

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Input files and in-house scripts for public transit air microbiome and resistome manuscrirpt.

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Name		Name	Last commit message	Last commit date
Latest commit History 2 Commits
180102_resfams_metadata_updated_v1.2.2.txt		180102_resfams_metadata_updated_v1.2.2.txt
add_resfam_metadata_to_arg_output.R		add_resfam_metadata_to_arg_output.R
assembly_combined_secondary_out_simple.txt		assembly_combined_secondary_out_simple.txt
binary_jaccard_panphlan_joined_tables_cacnes_w_ref.txt		binary_jaccard_panphlan_joined_tables_cacnes_w_ref.txt
binary_jaccard_panphlan_joined_tables_mluteus_new.txt		binary_jaccard_panphlan_joined_tables_mluteus_new.txt
combine_arg_plasmid_data.R		combine_arg_plasmid_data.R
combine_city_arg_data_coverage.R		combine_city_arg_data_coverage.R
contig_list_w_ARG.txt		contig_list_w_ARG.txt
convert_g_to_KO_Cacnes.R		convert_g_to_KO_Cacnes.R
convert_g_to_KO_Mluteus.R		convert_g_to_KO_Mluteus.R
create_domain_taxo_plot.R		create_domain_taxo_plot.R
create_rf_panphlan_plot.R		create_rf_panphlan_plot.R
density_plot.R		density_plot.R
draw_PCoA_bray_curtis.R		draw_PCoA_bray_curtis.R
draw_PCoA_panphlan_Cacnes.R		draw_PCoA_panphlan_Cacnes.R
draw_PCoA_panphlan_Mluteus.R		draw_PCoA_panphlan_Mluteus.R
lme4_richness_updated.R		lme4_richness_updated.R
lme4_shannon_updated.R		lme4_shannon_updated.R
merged_abundance_table_all_cities_domain.txt		merged_abundance_table_all_cities_domain.txt
merged_abundance_table_species_all_cities.cast.txt		merged_abundance_table_species_all_cities.cast.txt
merged_abundance_table_species_subsamp.txt		merged_abundance_table_species_subsamp.txt
metadata_Denver_new.txt		metadata_Denver_new.txt
metadata_HKG_new.txt		metadata_HKG_new.txt
metadata_London_new.txt		metadata_London_new.txt
metadata_NYC_new.txt		metadata_NYC_new.txt
metadata_Oslo_new.txt		metadata_Oslo_new.txt
metadata_Stockholm_new.txt		metadata_Stockholm_new.txt
metadata_new.txt		metadata_new.txt
mluteus_presence_wt_ref_Denver.txt		mluteus_presence_wt_ref_Denver.txt
mluteus_presence_wt_ref_HKG.txt		mluteus_presence_wt_ref_HKG.txt
mluteus_presence_wt_ref_London.txt		mluteus_presence_wt_ref_London.txt
mluteus_presence_wt_ref_NYC.txt		mluteus_presence_wt_ref_NYC.txt
mluteus_presence_wt_ref_Oslo.txt		mluteus_presence_wt_ref_Oslo.txt
mluteus_presence_wt_ref_Stockholm.txt		mluteus_presence_wt_ref_Stockholm.txt
no_contig_plasmid_chromo.pdf		no_contig_plasmid_chromo.pdf
pacnes_presence_wt_ref_Denver.txt		pacnes_presence_wt_ref_Denver.txt
pacnes_presence_wt_ref_HKG.txt		pacnes_presence_wt_ref_HKG.txt
pacnes_presence_wt_ref_London.txt		pacnes_presence_wt_ref_London.txt
pacnes_presence_wt_ref_NYC.txt		pacnes_presence_wt_ref_NYC.txt
pacnes_presence_wt_ref_Oslo.txt		pacnes_presence_wt_ref_Oslo.txt
pacnes_presence_wt_ref_Stockholm.txt		pacnes_presence_wt_ref_Stockholm.txt
panphlan_merged_distance_taxonomy_ref_info.txt		panphlan_merged_distance_taxonomy_ref_info.txt
panphlan_mluteus16_centroids_translated.fasta.emapper.annotations.txt		panphlan_mluteus16_centroids_translated.fasta.emapper.annotations.txt
panphlan_output_sample_list_w_city.txt		panphlan_output_sample_list_w_city.txt
panphlan_pacnes16_centroids_translated.fasta.emapper.annotations.txt		panphlan_pacnes16_centroids_translated.fasta.emapper.annotations.txt
perform_alpha_diversity_subsamp.R		perform_alpha_diversity_subsamp.R
plasflow_out_all_contigs_new_tax_only.txt		plasflow_out_all_contigs_new_tax_only.txt
plasmid_w_ARG_data_new.txt		plasmid_w_ARG_data_new.txt
plasmid_w_ARG_data_tally.txt		plasmid_w_ARG_data_tally.txt