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This script shows how to the dataset were analysed, and how the plots in the paper were made.

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LinuxCommands
LinuxCommands
 
 
code
code
 
 
documentation
documentation
 
 
.Renviron
.Renviron
 
 
.gitignore
.gitignore
 
 
3D_PCoA_Bray_Curtis.html
3D_PCoA_Bray_Curtis.html
 
 
3D_PCoA_Bray_Curtis.png
3D_PCoA_Bray_Curtis.png
 
 
3D_PCoA_Bray_Curtis.pptx
3D_PCoA_Bray_Curtis.pptx
 
 
ASV_sequence_list.txt
ASV_sequence_list.txt
 
 
ASV_venn_diagram.png
ASV_venn_diagram.png
 
 
ASV_venn_diagram.png.2024-06-28_01-35-26.log
ASV_venn_diagram.png.2024-06-28_01-35-26.log
 
 
ASV_venn_diagram.png.2024-06-28_03-22-01.log
ASV_venn_diagram.png.2024-06-28_03-22-01.log
 
 
ASV_venn_diagram.png.2024-06-28_03-22-19.log
ASV_venn_diagram.png.2024-06-28_03-22-19.log
 
 
ASV_venn_diagram.png.2024-06-28_22-45-16.log
ASV_venn_diagram.png.2024-06-28_22-45-16.log
 
 
ASV_venn_diagram.png.2024-06-28_22-46-33.log
ASV_venn_diagram.png.2024-06-28_22-46-33.log
 
 
ASV_venn_diagram.png.2024-08-11_22-41-27.log
ASV_venn_diagram.png.2024-08-11_22-41-27.log
 
 
ASV_venn_diagram.png.2024-08-11_22-42-42.log
ASV_venn_diagram.png.2024-08-11_22-42-42.log
 
 
Anova_Organic.xlsx
Anova_Organic.xlsx
 
 
Anova_inorganic.xlsx
Anova_inorganic.xlsx
 
 
Blast_analysis_notes.txt
Blast_analysis_notes.txt
 
 
Blast_result.txt
Blast_result.txt
 
 
Combined_PrototypeData(Inorganic_Data).csv
Combined_PrototypeData(Inorganic_Data).csv
 
 
DWS.Rproj
DWS.Rproj
 
 
Data_Sanky.xlsx
Data_Sanky.xlsx
 
 
Family_relative_abundance.png
Family_relative_abundance.png
 
 
Galaxy_blastn.table.tsv
Galaxy_blastn.table.tsv
 
 
MP_ANOVA.xlsx
MP_ANOVA.xlsx
 
 
MP_analysis.r
MP_analysis.r
 
 
MP_data.xlsx
MP_data.xlsx
 
 
Manifest_WW.txt
Manifest_WW.txt
 
 
MetData_Pathogen_removal.tsv
MetData_Pathogen_removal.tsv
 
 
Metadata.tsv
Metadata.tsv
 
 
MetadataWastewater.csv
MetadataWastewater.csv
 
 
PCoA_Genotype_Day.pdf
PCoA_Genotype_Day.pdf
 
 
PCoA_Weighted_UniFrac_Genotype_Day.pdf
PCoA_Weighted_UniFrac_Genotype_Day.pdf
 
 
Prototype_Analysis_Report.txt
Prototype_Analysis_Report.txt
 
 
Prototype_Inorganic_Removal.xlsx
Prototype_Inorganic_Removal.xlsx
 
 
Prototype_Removal.xlsx
Prototype_Removal.xlsx
 
 
Prototype_analysis.r
Prototype_analysis.r
 
 
Prototype_analysis.txt
Prototype_analysis.txt
 
 
README.md
README.md
 
 
Stat_table_Removal.csv
Stat_table_Removal.csv
 
 
Stat_table_Removal.xlsx
Stat_table_Removal.xlsx
 
 
Toxicity_data_graphene_for_sanky_plot.csv
Toxicity_data_graphene_for_sanky_plot.csv
 
 
VennDiagram.2024-06-28_00-59-13.log
VennDiagram.2024-06-28_00-59-13.log
 
 
VennDiagram.2024-08-09_10-58-15.log
VennDiagram.2024-08-09_10-58-15.log
 
 
VennDiagram.2024-08-12_08-04-42.log
VennDiagram.2024-08-12_08-04-42.log
 
 
WastewaterProof.nb.html
WastewaterProof.nb.html
 
 
WastewaterProof.rmd
WastewaterProof.rmd
 
 
adonis_results.xlsx
adonis_results.xlsx
 
 
anova_results.txt
anova_results.txt
 
 
anova_results_inorganic.txt
anova_results_inorganic.txt
 
 
anova_results_mp.xlsx
anova_results_mp.xlsx
 
 
anova_results_mp_PFOA.xlsx
anova_results_mp_PFOA.xlsx
 
 
anova_results_mp_PFOA_PFOS.xlsx
anova_results_mp_PFOA_PFOS.xlsx
 
 
anova_results_mp_PFOS.xlsx
anova_results_mp_PFOS.xlsx
 
 
anova_results_organic_COD_absent.txt
anova_results_organic_COD_absent.txt
 
 
blast_info.csv
blast_info.csv
 
 
blast_info_mapped.csv
blast_info_mapped.csv
 
 
blast_info_mapped_to_features.csv
blast_info_mapped_to_features.csv
 
 
blast_info_mapped_to_features2.csv
blast_info_mapped_to_features2.csv
 
 
blast_info_mappped_to_features.csv
blast_info_mappped_to_features.csv
 
 
blastn_output.csv
blastn_output.csv
 
 
dna-sequences-250.fasta
dna-sequences-250.fasta
 
 
family_top10.csv
family_top10.csv
 
 
family_top15.csv
family_top15.csv
 
 
feature-table-250.tsv
feature-table-250.tsv
 
 
feature_table.csv
feature_table.csv
 
 
filtered4_blast_output.txt
filtered4_blast_output.txt
 
 
filtered_blast_output.txt
filtered_blast_output.txt
 
 
filtered_table.qza
filtered_table.qza
 
 
frequency_genus-table.tsv
frequency_genus-table.tsv
 
 
genus_abundance_plot.png
genus_abundance_plot.png
 
 
genus_abundance_with_error_bars.png
genus_abundance_with_error_bars.png
 
 
genus_abundance_with_pies.png
genus_abundance_with_pies.png
 
 
genus_relative_abundance.png
genus_relative_abundance.png
 
 
genus_top10.csv
genus_top10.csv
 
 
genus_top15.csv
genus_top15.csv
 
 
graphene_toxicity.r
graphene_toxicity.r
 
 
heatmap.png
heatmap.png
 
 
heatmap_for_powerpoint.pdf
heatmap_for_powerpoint.pdf
 
 
heatmap_for_powerpoint.svg
heatmap_for_powerpoint.svg
 
 
improved_heatmap.pdf
improved_heatmap.pdf
 
 
improved_heatmap.png
improved_heatmap.png
 
 
improved_venn_diagram.png.2024-06-28_13-47-00.log
improved_venn_diagram.png.2024-06-28_13-47-00.log
 
 
insertion-tree.qza
insertion-tree.qza
 
 
original_data_filtered.csv
original_data_filtered.csv
 
 
posthoc_results_organic_COD_absent.txt
posthoc_results_organic_COD_absent.txt
 
 
query_to_sample_mapping.csv
query_to_sample_mapping.csv
 
 
read-stats.tsv
read-stats.tsv
 
 
removal_efficiency.pptx
removal_efficiency.pptx
 
 
residual_plot.pdf
residual_plot.pdf
 
 
sample_metadata.csv
sample_metadata.csv
 
 
significant_hits.tsv
significant_hits.tsv
 
 
tax_rel_abun_pf_gen_top10.csv
tax_rel_abun_pf_gen_top10.csv
 
 
taxonomy.qza
taxonomy.qza
 
 
taxonomy.tsv
taxonomy.tsv
 
 
top_15_genera_abundance.csv
top_15_genera_abundance.csv
 
 
top_15_genera_abundance_by_genotype_and_day.csv
top_15_genera_abundance_by_genotype_and_day.csv
 
 
venn.pdf
venn.pdf
 
 

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DWS

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This script shows how to the dataset were analysed, and how the plots in the paper were made.

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