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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.

Getting Started

First build the image:

docker pull "waldronlab/curatedmetagenomicanalyses"

Then run a container based on the image with your password:

docker run -d -p 80:8888 --name cma \
  waldronlab/curatedmetagenomicanalyses

Visit localhost/lab in your browser.

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)