This is the repository for the workshop at MiCom 2021 about taxonomic correlation analyses in metagenomics using R.
- Raw data directory with example data and meta data about species and pathway abundances in helthy and cancer subjects based on curatedMetagenomicData
- Installation script for R packages including BAnOCC, SpiecEasi and drake
- Dockerfile to create a container with all tools needed for the analysis. This is based on rocker/verse containing RStudio Server.
- Makefile to build and run the docker container
- Run script to run the drake workflow and build the HTML report
- Setup script to create the R environment with loaded packages and default options
- Drake plans defining an example analysis workflow
- Library with wrapper functions to call various correlation methods with a uniform interface
- BibTeX containing literature used
Clone this repository with these shell commands. GNU Make can be used to build and run the docker container:
git clone https://github.com/bioinformatics-leibniz-hki/correlation-workshop
cd correlation-workshop
make
This will deploy a webserver which can be accessed in your browser.
Go to the URL displayed and log in to RStudio Server using username rstudio and password password.