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repository_map.txt
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Panel github_script plot
1A MGX_and_MTX_QC.Rmd ribo_deplete_versus_non_deplete.pdf
1B MGX_and_MTX_QC.Rmd RNA_kraken_sorensen_boxplot.pdf
1C MGX_and_MTX_QC.Rmd RNA_OG_pearson_boxplot.pdf
1D MGX_and_MTX_QC.Rmd mtx_read_count_stats.pdf
1E MGX_and_MTX_QC.Rmd full_cohort_mtx_rRNA_stats.pdf
1F MGX_and_MTX_QC.Rmd [A-Z]*_bact_cov_plot.pdf
1G MGX_and_MTX_QC.Rmd [A-Z]*_fungi_cov_plot.pdf
1H MGX_and_MTX_QC.Rmd genomic_region_RNA_mapping_M_globosa_plot.pdf
2A niche_specific_signatures.Rmd site_median_abun_barplot.pdf
2B niche_specific_signatures.Rmd mgx_taxa_balloon_plot.pdf; mtx_taxa_balloon_plot.pdf
2C niche_specific_signatures.Rmd contributional_diversity.pdf
2D niche_specific_signatures.Rmd staphyloferrin_Tw_pathway_vs_mtx_plot
3A species_level_DE.Rmd M_restricta_Sc_Ch_DE_volcano.pdf
3B species_level_DE.Rmd M_restricta_Sc_Ch_DE_NES_KEGG.pdf
3C species_level_DE.Rmd microbial_Sc_vs_Ch_DE_tally_barplot.pdf
3E left species_level_DE.Rmd invivo_invitro_PCA_batch_corrected.pdf
3E right species_level_DE.Rmd S_epi_DE_tally_barplot.pdf
4A Figure4_SuppFig14_15.qmd Figure4A.pdf
4B Figure4_SuppFig14_15.qmd Figure4B.pdf
4C Figure4_SuppFig14_15.qmd Figure4C.pdf
4D Figure4_SuppFig14_15.qmd Figure4D.pdf
5A microbe-microbe_interactions.Rmd hmm_AM_heatmap.pdf
5B microbe-microbe_interactions.Rmd hmm_AM_species_heatmap.pdf
5C https://figshare.com/articles/dataset/Foldseek_and_DALI_results_for_the_Malassezia_restricta_protein_DNF11_2196/27860994?file=50645928
5D HIBIT_ELISA_analysis.Rmd IL1B_HIBIT_plot.pdf; IL1B_ELISA_plot.pdf
S1A Supp_sequencing_stats_QC.Rmd pilot_cohort_mtx_vs_humann3_boxplot.pdf
S1B Supp_sequencing_stats_QC.Rmd main_cohort_dv200_boxplot.pdf
S1C Supp_sequencing_stats_QC.Rmd mgx_read_stats_boxplot.pdf
S1D Supp_sequencing_stats_QC.Rmd mtx_mgx_non_human_percent_boxplot.pdf
S1E Supp_sequencing_stats_QC.Rmd mtx_mgx_proportion_microbial_annotated.pdf
S2B controlling_artefacts.Rmd mgx_corr_contam_heatmap.pdf
S2C controlling_artefacts.Rmd mtx_minimizer_microbe_ratio_plot.pdf
S3 rarefaction.Rmd mtx_microbe_*_rarefaction.pdf
S4 mtx_vs_mgx_counts_species_level.Rmd core_common_taxa_RNA_v_DNA.pdf
S5 transcriptional_activity_species.Rmd bacteria_species_transcriptional_activity .pdf
S6 transcriptional_activity_species.Rmd fungal_species_transcriptional_activity.pdf
S7 species_abundance_barplots.Rmd Ac_species_abundance_boxplot.pdf
S8 OG_level_DE.Rmd Supp_between_site_GSEA_NES_plots.pdf
S9A OG_level_DE.Rmd OG_Ch_vs_Vf_DE_volcano.pdf
S9B OG_level_DE.Rmd OG_Tw_vs_Vf_DE_volcano.pdf
S10A niche_specific_signatures.Rmd mtx_pathway_dominated_boxplot_padj.pdf
S10B niche_specific_signatures.Rmd beta_ox_pathway_plots.pdf
S10C niche_specific_signatures.Rmd galactose_deg_pathway_plots.pdf
S10D niche_specific_signatures.Rmd Arg_biosyn_pathway_plots.pdf
S11A species_level_DE.Rmd invivo_invitro_in_house_PCA.pdf
S11B species_level_DE.Rmd invivo_invitro_PCA_batch_corrected_zoomed.pdf
S12 species_level_DE.Rmd S_epi_Seb_vs_invitro_NES_plot.pdf
S13A top species_level_DE.Rmd S_epi_Tw_vs_all_log_phase_GSEA_slim_NES_barplot.pdf
S13A bottom species_level_DE.Rmd S_epi_Tw_vs_all_OS_GSEA_slim_NES_barplot.pdf
S13B top species_level_DE.Rmd Tw_vs_all_log_phase_l2fc_metal_ion_clust_barplot.pdf
S13B bottom species_level_DE.Rmd Tw_vs_all_OS_l2fc_Cu_ion_binding_barplot.pdf
S14A Figure4_SuppFig14_15.qmd SuppFig14A
S14B Figure4_SuppFig14_15.qmd SuppFig14B
S14C Figure4_SuppFig14_15.qmd SuppFig14C
S15 Figure4_SuppFig14_15.qmd SuppFig15
S16A microbe-microbe_interactions.Rmd lacticin481_presence_clr_boxplot.pdf
S16B microbe-microbe_interactions.Rmd lacticin481_presence_rna_k2_counts_boxplot.pdf
S16C microbe-microbe_interactions.Rmd thiopeptide_presence_C_acnes_clr.pdf
S16D microbe-microbe_interactions.Rmd thiopeptide_presence_rna_k2_counts.pdf
S17 microbe-microbe_interactions.Rmd thiopeptide_AA_heatmaps.pdf
S18 microbe-microbe_interactions.Rmd lactococcin972_AA_heatmaps.pdf
S19 microbe-microbe_interactions.Rmd halocin_AA_heatmaps.pdf
S20A human_reads_analysis.Rmd main_cohort_hg38_read_pairs_boxplot.pdf
S20B human_reads_analysis.Rmd all_studies_hg38_prop_boxplot.pdf
S21 gsva_pathway_analysis.Rmd immune_S_cap_clr_Ch_corr.pdf
S22A microbe-microbe_interactions.Rmd M_res_mtx_vs_C_acnes_mgx_Sc_corr_volcano.pdf
S22B microbe-microbe_interactions.Rmd M_res_DNF11_2196_vs_C_acnes_mgx_scatter.pdf
S22C microbe-microbe_interactions.Rmd M_res_DNF11_2196_vs_M_res_mgx_scatter.pdf
S22D microbe-microbe_interactions.Rmd M_res_abun_vs_C_acnes_abun_scatter.pdf
S22E microbe-microbe_interactions.Rmd C_acnes_mtx_vs_C_gran_mgx_Ch_corr_volcano.pdf
S22F microbe-microbe_interactions.Rmd C_acnes_AAT83849_vs_C_granulosum_mgx_scatter.pdf
S22G microbe-microbe_interactions.Rmd C_acnes_AAT83849_vs_C_acnes_mgx_scatter.pdf
S23 mock_comm_DNA_analysis.Rmd trizol_vs_EZ1_species_DNA_corr.pdf