- recipe bioconductor-microbiomebenchmarkdata
Datasets for benchmarking in microbiome research
The MicrobiomeBenchmarkData package provides functionality to access microbiome datasets suitable for benchmarking. These datasets have some biological truth, which allows to have expected results for comparison. The datasets come from various published sources and are provided as TreeSummarizedExperiment objects. Currently, only datasets suitable for benchmarking differential abundance methods are available.
- package bioconductor-microbiomebenchmarkdata¶
- depends bioconductor-biocfilecache:
- depends bioconductor-data-packages:
- depends bioconductor-s4vectors:
- depends bioconductor-summarizedexperiment:
- depends bioconductor-treesummarizedexperiment:
- depends curl:
- depends r-ape:
- depends r-base:
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-microbiomebenchmarkdata and update with:: mamba update bioconductor-microbiomebenchmarkdata
To create a new environment, run:
mamba create --name myenvname bioconductor-microbiomebenchmarkdata
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-microbiomebenchmarkdata:<tag> (see `bioconductor-microbiomebenchmarkdata/tags`_ for valid values for ``<tag>``)