- recipe bioconductor-mia
Microbiome analysis
- Homepage:
- License:
Artistic-2.0 | file LICENSE
- Recipe:
mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization.
- package bioconductor-mia¶
- versions:
1.8.0-0,1.6.0-0,1.2.2-0,1.0.2-0- depends bioconductor-biocgenerics:
>=0.46.0,<0.47.0- depends bioconductor-biocparallel:
>=1.34.0,<1.35.0- depends bioconductor-biostrings:
>=2.68.0,<2.69.0- depends bioconductor-decipher:
>=2.28.0,<2.29.0- depends bioconductor-decontam:
>=1.20.0,<1.21.0- depends bioconductor-delayedarray:
>=0.26.0,<0.27.0- depends bioconductor-delayedmatrixstats:
>=1.22.0,<1.23.0- depends bioconductor-dirichletmultinomial:
>=1.42.0,<1.43.0- depends bioconductor-iranges:
>=2.34.0,<2.35.0- depends bioconductor-multiassayexperiment:
>=1.26.0,<1.27.0- depends bioconductor-s4vectors:
>=0.38.0,<0.39.0- depends bioconductor-scater:
>=1.28.0,<1.29.0- depends bioconductor-scuttle:
>=1.10.0,<1.11.0- depends bioconductor-singlecellexperiment:
>=1.22.0,<1.23.0- depends bioconductor-summarizedexperiment:
>=1.30.0,<1.31.0- depends bioconductor-treesummarizedexperiment:
>=2.8.0,<2.9.0- depends r-ape:
- depends r-base:
>=4.3,<4.4.0a0- depends r-dplyr:
- depends r-mass:
- depends r-rlang:
- depends r-tibble:
- depends r-tidyr:
- depends r-vegan:
- requirements:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
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-mia and update with:: mamba update bioconductor-mia
To create a new environment, run:
mamba create --name myenvname bioconductor-mia
with
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-mia:<tag> (see `bioconductor-mia/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-mia/README.html)
