recipe bioconductor-pathostat

PathoStat Statistical Microbiome Analysis Package

Homepage:

https://bioconductor.org/packages/3.16/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:

1.24.0-0,  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, 

1.24.0-0,  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:

• bioconductor-biocstyle >=2.26.0,<2.27.0

• bioconductor-complexheatmap >=2.14.0,<2.15.0

• bioconductor-deseq2 >=1.38.0,<1.39.0

• bioconductor-edger >=3.40.0,<3.41.0

• bioconductor-limma >=3.54.0,<3.55.0

• bioconductor-phyloseq >=1.42.0,<1.43.0

• r-ape

• r-base >=4.2,<4.3.0a0

• r-corpcor

• r-devtools

• r-dplyr

• r-dt

• r-ggplot2

• r-glmnet

• r-gmodels

• r-knitr

• r-matrixstats

• r-plotly

• r-plyr

• r-rcolorbrewer

• r-rentrez

• r-reshape2

• r-rocr

• r-scales

• r-shiny

• r-shinyjs

• r-tidyr

• r-vegan

• r-webshot

• r-xml

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-pathostat

and update with:

conda update bioconductor-pathostat

or use the docker container:

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

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

Download stats

Link to this page

Render an badge with the following MarkDown:

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