💻 📊 Analyses to recreate the results in the manuscript "Rumen bacterial community structure impacts feed efficiency in beef cattle" by Paz et al. 2017 in JAS. The analyses are separated into several R Markdown files.
Follow the instructions below to setup the same environment used to analyze the data and render the R Markdown files. Adhere to the delineated order as succeeding R Markdown files depend on previous results. If working in a server, setup X11 forwarding.
1. data_curation.Rmd
2. generate_OTU_table.Rmd
3. qc_bacterial.Rmd
4. feed_efficiency_phenotype.Rmd
5. alpha_diversity.Rmd
6. beta_diversity.Rmd
7. differential_OTUs.Rmd
8. differentially_abundant_families.Rmd
9. forward_stepwise_regression.Rmd
10. forward_stepwise_regression_family.Rmd
Due to licensing constraints, USEARCH could not be included in the setup. The current dataset requires more than the 4Gb RAM allowed in the no-charge 32-bit version, thus the paid license Linux USEARCH 64-bit version was used. USEARCH outputs required in the analyses are provided in the usearch_outputs directory.
Create the environment
Clone the github repository and run the setup.sh script
- git clone https://github.com/enriquepaz/RumenMicrobiome_Beef.git
- cd RumenMicrobiome_Beef
- ./setup.sh
Render R Markdown files
Within the RumenMicrobiome_Beef directory
- source anaconda/bin/activate qiimemothur
- anaconda/envs/r/bin/Rscript -e "rmarkdown::render('file[1-8].Rmd')"