Package Recipe 'bioconductor-pathostat'

recipe bioconductor-pathostat

PathoStat Statistical Microbiome Analysis Package

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/PathoStat.html
License:: GPL (>= 2)
Recipe:: /bioconductor-pathostat/meta.yaml
Links:: 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¶

Versions:

1.36.0-0, 1.32.0-0, 1.28.0-0, 1.26.0-0, 1.24.0-0, 1.20.0-0, 1.18.0-0, 1.16.0-1, 1.16.0-0,

1.36.0-0, 1.32.0-0, 1.28.0-0, 1.26.0-0, 1.24.0-0, 1.20.0-0, 1.18.0-0, 1.16.0-1, 1.16.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-1, 1.8.4-0, 1.6.1-0, 1.4.1-0

Depends:

on bioconductor-biocstyle >=2.38.0,<2.39.0
on bioconductor-complexheatmap >=2.26.0,<2.27.0
on bioconductor-deseq2 >=1.50.0,<1.51.0
on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-phyloseq >=1.54.0,<1.55.0
on r-ape
on r-base >=4.5,<4.6.0a0
on r-corpcor
on r-devtools
on r-dplyr
on r-dt
on r-ggplot2
on r-glmnet
on r-gmodels
on r-knitr
on r-matrixstats
on r-plotly
on r-plyr
on r-rcolorbrewer
on r-rentrez
on r-reshape2
on r-rocr
on r-scales
on r-shiny
on r-shinyjs
on r-tidyr
on r-vegan
on r-webshot
on r-xml

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-pathostat

to add into an existing workspace instead, run:

pixi add bioconductor-pathostat

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-pathostat

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-pathostat

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-pathostat:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-pathostat/README.html)