/release_mice_aspergillus_infection_lung_project

code for the paper "The murine lung microbiome is dysbalanced by the human pathogenic fungus Aspergillus fumigatus resulting in enrichment of anaerobic bacteria"

Primary LanguageRMIT LicenseMIT

Data

  • raw_data/lung_phyloseq.Rdata: lotus2(v2.23, uparse)
  • raw_data/gut_phyloseq.Rdata: lotus2(v2.23, uparse)
  • raw_data/lung_mebo_pre.csv: lung metabolome profiles
  • raw_data/plasma_mebo_pre.csv: plasma metabolome profiles

Command

set cpu number

edit 0.make_targets_config.R at first, then

Rscript make_targets_config.R

run pipeline

Rscript targets.R