recipe bioconductor-pathostat

PathoStat Statistical Microbiome Analysis Package



GPL (>= 2)




biotools: pathostat, doi: 10.1038/nmeth.3252

The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis.

package bioconductor-pathostat

(downloads) docker_bioconductor-pathostat



depends bioconductor-biocstyle:


depends bioconductor-complexheatmap:


depends bioconductor-deseq2:


depends bioconductor-edger:


depends bioconductor-limma:


depends bioconductor-phyloseq:


depends r-ape:

depends r-base:


depends r-corpcor:

depends r-devtools:

depends r-dplyr:

depends r-dt:

depends r-ggplot2:

depends r-glmnet:

depends r-gmodels:

depends r-knitr:

depends r-matrixstats:

depends r-plotly:

depends r-plyr:

depends r-rcolorbrewer:

depends r-rentrez:

depends r-reshape2:

depends r-rocr:

depends r-scales:

depends r-shiny:

depends r-shinyjs:

depends r-tidyr:

depends r-vegan:

depends r-webshot:

depends r-xml:



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-pathostat

and update with::

   mamba update bioconductor-pathostat

To create a new environment, run:

mamba create --name myenvname bioconductor-pathostat

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-pathostat/tags`_ for valid values for ``<tag>``)

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