This repository provides biologically relevant analyses using the curatedMetagenomicData package, both using R/Bioconductor and using Python. You can run both R and Python analyses locally in the provided Docker container, or on the Cloud for free.
Running locally using Docker
Requirements
You need Docker.
Running locally without Docker
Start with an installation of the current version of Bioconductor (see https://bioconductor.org/install/). Older versions probably will not work. Installation directly from GitHub requires first installing the remotes
package, then:
BiocManager::install("waldronlab/curatedMetagenomicDataAnalyses", dependencies = TRUE)
Analyses
R Vignettes
- Create datasets for machine learning
- Exploration of the liver cirrhosis dataset
- Select all colorectal cancer patients and create a cohort table, calculate prevalence of all species found in their stool microbiomes and create a dynamic searchable html table
- Meta-analysis of age-related microbial species using cMD3
- Meta-analysis of sex-related microbial species using cMD3
- NUI Galway Metagenomics Workshop
Supplementary Materials
- Installing Python dependencies in Linux (Python notebook)