AMAC002_salmonella_trial

Analysis repository of the experiment 6.3 on salmonella infection in broilers. The downstream analyses are split in multiple steps.

1. Prepare data

The first step fetches all relevant data and generates a data.Rdata file in the data directory.

• Rmd code: https://github.com/3d-omics/AMAC002_salmonella_trial/blob/main/1-prepare_data.Rmd
• HTML render: https://github.com/3d-omics/AMAC002_salmonella_trial/blob/main/1-prepare_data.html

2. Genome catalogue overview

Overview of the taxonomic, phylogenetic and functional attributes of the genome catalogue

• Rmd code: https://github.com/3d-omics/AMAC002_salmonella_trial/blob/main/2-genome_catalogue_overview.Rmd
• HTML render: https://github.com/3d-omics/AMAC002_salmonella_trial/blob/main/2-genome_catalogue_overview.html

3. Composition overview

Overview of the composition and diversity of microbial communities.

• Rmd code: https://github.com/3d-omics/AMAC002_salmonella_trial/blob/main/3-composition_overview.Rmd
• HTML render: https://github.com/3d-omics/AMAC002_salmonella_trial/blob/main/3-composition_overview.html

4. Differential abundance between treatments

• Rmd code: https://github.com/3d-omics/AMAC002_salmonella_trial/blob/main/5-hmsc.Rmd
• HTML render: https://github.com/3d-omics/AMAC002_salmonella_trial/blob/main/5-hmsc.html