Registration Open for Bioc2024 July 24-26


PathoStat Statistical Microbiome Analysis Package

Bioconductor version: Release (3.19)

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 "4.4") and enter:

if (!require("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:

PathoStat intro HTML R Script
Reference Manual PDF


biocViews GraphAndNetwork, ImmunoOncology, Metagenomics, Microarray, Microbiome, PatternLogic, PrincipalComponent, RNASeq, Sequencing, Software, Visualization
Version 1.30.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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
System Requirements
Bug Reports
See More
Suggests rmarkdown, testthat
Linking To
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package PathoStat_1.30.0.tar.gz
Windows Binary
macOS Binary (x86_64) PathoStat_1.30.0.tgz
macOS Binary (arm64) PathoStat_1.30.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats