DOI: 10.18129/B9.bioc.PathoStat    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see PathoStat.

PathoStat Statistical Microbiome Analysis Package

Bioconductor version: 3.10

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.

Author: Solaiappan Manimaran <manimaran_1975 at>, Matthew Bendall <bendall at>, Sandro Valenzuela Diaz <sandrolvalenzuelad at>, Eduardo Castro <castronallar at>, Tyler Faits <tfaits at>, Yue Zhao <jasonzhao0307 at>, Anthony Nicholas Federico <anfed at>, W. Evan Johnson <wej at>

Maintainer: Solaiappan Manimaran <manimaran_1975 at>, Yue Zhao <jasonzhao0307 at>

Citation (from within R, enter citation("PathoStat")):


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



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biocViews GraphAndNetwork, ImmunoOncology, Metagenomics, Microarray, Microbiome, PatternLogic, PrincipalComponent, RNASeq, Sequencing, Software, Visualization
Version 1.12.0
In Bioconductor since BioC 3.4 (R-3.3) (3.5 years)
License GPL (>= 2)
Depends R (>= 3.5)
Imports limma, corpcor, matrixStats, reshape2, scales, ggplot2, rentrez, DT, tidyr, plyr, dplyr, phyloseq, shiny, stats, methods, XML, graphics, utils, BiocStyle, edgeR, DESeq2, ComplexHeatmap, plotly, webshot, vegan, shinyjs, glmnet, gmodels, ROCR, RColorBrewer, knitr, devtools, ape
Suggests rmarkdown, testthat
Depends On Me
Imports Me
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