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Application of metagenomics and metabolomics to assess the effects of urban polycyclic aromatic hydrocarbon exposure on the skin microbiota cutotypes

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decontam_genomes
decontam_genomes
 
 
ARG_family_w_cutotype.txt
ARG_family_w_cutotype.txt
 
 
BC_resistome_matrix.txt
BC_resistome_matrix.txt
 
 
BC_tax_matrix.txt
BC_tax_matrix.txt
 
 
GRID_input_new_p10.txt
GRID_input_new_p10.txt
 
 
PCoA_coordinates_kraken2.txt
PCoA_coordinates_kraken2.txt
 
 
PCoA_coordinates_kraken2_w_ctypes.txt
PCoA_coordinates_kraken2_w_ctypes.txt
 
 
PCoA_coordinates_kraken2_w_meta.txt
PCoA_coordinates_kraken2_w_meta.txt
 
 
Procrustes_analysis_meta_edit.R
Procrustes_analysis_meta_edit.R
 
 
README.md
README.md
 
 
beta_PCoA_adonis2_kraken2.R
beta_PCoA_adonis2_kraken2.R
 
 
beta_PCoA_adonis2_shortbred.R
beta_PCoA_adonis2_shortbred.R
 
 
bracken2_all_samples_long_percentage_wide_newer_top12.txt
bracken2_all_samples_long_percentage_wide_newer_top12.txt
 
 
bracken2_all_samples_wide_0_00001_adjusted_for_human_clean_no_con.txt
bracken2_all_samples_wide_0_00001_adjusted_for_human_clean_no_con.txt
 
 
bracken2_all_samples_wide_0_00001_adjusted_for_human_clean_no_con_122.txt
bracken2_all_samples_wide_0_00001_adjusted_for_human_clean_no_con_122.txt
 
 
bracken_table_species_subsamp_transposed.txt
bracken_table_species_subsamp_transposed.txt
 
 
c_acnes_smeg_long.txt
c_acnes_smeg_long.txt
 
 
c_acnes_smeg_matrix.txt
c_acnes_smeg_matrix.txt
 
 
c_acnes_smeg_matrix_cluster.txt
c_acnes_smeg_matrix_cluster.txt
 
 
c_acnes_smeg_matrix_cutotype.txt
c_acnes_smeg_matrix_cutotype.txt
 
 
c_acnes_smeg_matrix_edited_no_rows_cols.txt
c_acnes_smeg_matrix_edited_no_rows_cols.txt
 
 
calculate_contributional_diversity_per_city.R
calculate_contributional_diversity_per_city.R
 
 
combined_shortbred_output_wide_family_level.txt
combined_shortbred_output_wide_family_level.txt
 
 
combined_shortbred_output_wide_transposed.txt
combined_shortbred_output_wide_transposed.txt
 
 
compile_kraken_output_count.R
compile_kraken_output_count.R
 
 
contributional_diversity_core_pathway_per_cutotype_new.txt
contributional_diversity_core_pathway_per_cutotype_new.txt
 
 
cutotype_PAM_PCoA_coords.txt
cutotype_PAM_PCoA_coords.txt
 
 
cutotype_host_factors.txt
cutotype_host_factors.txt
 
 
draw_cutotype_host_factor.R
draw_cutotype_host_factor.R
 
 
draw_fungal_density.R
draw_fungal_density.R
 
 
draw_maaslin_output.R
draw_maaslin_output.R
 
 
draw_top12_plot.R
draw_top12_plot.R
 
 
findfungi_output_normalized.txt
findfungi_output_normalized.txt
 
 
genome_completeness_ko_genome_size.R
genome_completeness_ko_genome_size.R
 
 
humann_pathabundance_relab_stratified_C1.txt
humann_pathabundance_relab_stratified_C1.txt
 
 
humann_pathabundance_relab_stratified_C2.txt
humann_pathabundance_relab_stratified_C2.txt
 
 
identified_core_humann2_pathway_by_city.R
identified_core_humann2_pathway_by_city.R
 
 
identify_clustering_PAM.R
identify_clustering_PAM.R
 
 
joined_genefamilies_table_unstratified_cpm_ko_122.txt
joined_genefamilies_table_unstratified_cpm_ko_122.txt
 
 
joined_pathwayabundance_relab_stratified_fixed.tsv
joined_pathwayabundance_relab_stratified_fixed.tsv
 
 
m_luteus_smeg_long.txt
m_luteus_smeg_long.txt
 
 
m_luteus_smeg_matrix.txt
m_luteus_smeg_matrix.txt
 
 
m_luteus_smeg_matrix_cluster.txt
m_luteus_smeg_matrix_cluster.txt
 
 
m_luteus_smeg_matrix_cutotype.txt
m_luteus_smeg_matrix_cutotype.txt
 
 
m_luteus_smeg_matrix_no_col_no_row.txt
m_luteus_smeg_matrix_no_col_no_row.txt
 
 
matrix_order_cutotype.txt
matrix_order_cutotype.txt
 
 
matrix_order_species.txt
matrix_order_species.txt
 
 
merged_abundance_table_species_subsamp.txt
merged_abundance_table_species_subsamp.txt
 
 
meta_new.txt
meta_new.txt
 
 
meta_pahoh_cutotype.txt
meta_pahoh_cutotype.txt
 
 
meta_pahoh_new_nospecialcharacter.txt
meta_pahoh_new_nospecialcharacter.txt
 
 
meta_sample_city_cutotype.txt
meta_sample_city_cutotype.txt
 
 
meta_sample_city_only.txt
meta_sample_city_only.txt
 
 
number_ko_genome_completeness.txt
number_ko_genome_completeness.txt
 
 
pairwise_BC_type.txt
pairwise_BC_type.txt
 
 
path_cast.txt
path_cast.txt
 
 
perform_alpha_diversity_subsamp_edit.R
perform_alpha_diversity_subsamp_edit.R
 
 
plot_grid_heatmap_edit.R
plot_grid_heatmap_edit.R
 
 
prevalence_count_histogram_plot.txt
prevalence_count_histogram_plot.txt
 
 
shannon_diversity_rarefied_samples_bracken_subsamp.txt
shannon_diversity_rarefied_samples_bracken_subsamp.txt
 
 
significant_results_for_maaslin_humann_pathway_plot.txt
significant_results_for_maaslin_humann_pathway_plot.txt
 
 
smeg_heatmap.R
smeg_heatmap.R
 
 
test_matrix.txt
test_matrix.txt
 
 
test_matrix_no_row_col.txt
test_matrix_no_row_col.txt
 
 
top12findfungi.txt
top12findfungi.txt
 
 
top_taxonomy_findfungi_edit.R
top_taxonomy_findfungi_edit.R
 
 

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skin_microbiota_pah2

Skin microbiota differentiates into distinct cutotypes with unique functional capabilities upon polycyclic aromatic hydrocarbon exposure

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Application of metagenomics and metabolomics to assess the effects of urban polycyclic aromatic hydrocarbon exposure on the skin microbiota cutotypes

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