About

Structure

Custom processing/analysis/plotting scripts used for "XX".

R/

Contains code of the R-package superheat which was slightly modified to accept additional arguments such as legend title and linkage method for hclust.

Scripts/

• MIC value processing
  • AST_process/10k_bacs_MIC_processing_v2.R
• Parsing Kraken reports
  • Taxonomy/parse_kraken_report.py
• NCBI taxonomy from taxa assigned by Kraken
  • Utils/get_full_tax.R
• Filter samples by taxonomy and assembly quality
  • Utils/filter_samples.R
• Pan-genomes
  • Centroid HMMs
    • Pan_genome/train_HMMs.py
  • Centroid rates simulation
    • Pan_genome/estimate_gene_rates.py
  • Further analyses
    • Create *.rds data for scripts below
      • SubProject_Pangenomes/scripts/create_meta.R
      • SubProject_Pangenomes/scripts/create_res_profiles.R
    • Some utils
      • SubProject_Pangenomes/scripts/utils.R
    • Krona plot
      • SubProject_Pangenomes/scripts/plot_tax_krona.R
    • Processed resfams/essential genes mapping to centroids
      • SubProject_Pangenomes/scripts/map_centroids2hits.py
    • Processing essential gene hits
      • SubProject_Pangenomes/scripts/process_essential_gene_hits.R
    • Plotting essential gene hits
      • SubProject_Pangenomes/scripts/plot_essential_gene_hits.R
    • MSA of essential genes
      • SubProject_Pangenomes/scripts/msa_essential_genes.py
      • SubProject_Pangenomes/scripts/cat_msa.py
    • Process resfams hits
      • SubProject_Pangenomes/scripts/process_resfams_hits.R
    • Plot resfams hits
      • SubProject_Pangenomes/scripts/plot_resfams_hits.R
    • Plot MLST summary
      • SubProject_Pangenomes/scripts/plot_mlst_sum.R
    • Assembly quality plot
      • SubProject_Pangenomes/scripts/plot_assembly_quali.R
    • Centroid rates plot
      • SubProject_Pangenomes/scripts/plot_pg_centroid_rates.R
    • Pan-genome size overview
      • SubProject_Pangenomes/scripts/plot_pg_size_ov.R
    • Plot RaXML tree
      • SubProject_Pangenomes/scripts/plot_raxml.R
• Stat. analysis w/o genomic data
  • Res. vs. date (WMW tests)
    • SubProject_ClassStat/Pipeline/scripts/data_analysis/res_date_tests.R
  • Plot results
    • SubProject_ClassStat/Pipeline/scripts/data_analysis/res_date_tests_plots.R
  • Drug correlations (w/ plot)
    • SubProject_ClassStat/Pipeline/scripts/data_analysis/drug_cor.R
• Resistance associations
  • Prediction/
    • Only EIGENSTRAT results on whole dataset were used