Chicken LMD compilation for method development

Analyses of all the metagenomic microsamples from chicken

Bioinformatic procedures

Data processing to generate the count data was conducted using the following Snakemake pipeline: mg_quant. Data analysis procedures source from the outputs of this pipeline.

Analysis procedures

The raw code used for data analysis is in the Rmd files stored in the root directory of this repository, while the bookdown-rendered webbook is available at: 3d-omics.github.io/ANMI014_chicken_LMD_methods

While the webbook provides a user-friendly overview of the procedures, analyses can be directly reproduced using the Rmd documents. Note that the code chunks that require heavy computation have been tuned off using 'eval=FALSE'. To re-render the webbook, you can use the following code:

library(bookdown)
library(htmlwidgets)
library(webshot)

render_book(input = ".", output_format = "bookdown::gitbook", output_dir = "docs")

ace4cec (Initial commit)