PathoStat

This is the released version of PathoStat; for the devel version, see PathoStat.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4

PathoStat Statistical Microbiome Analysis Package

Bioconductor version: Release (3.23)

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 hotmail.com>, Matthew Bendall <bendall at gwmail.gwu.edu>, Sandro Valenzuela Diaz <sandrolvalenzuelad at gmail.com>, Eduardo Castro <castronallar at gmail.com>, Tyler Faits <tfaits at gmail.com>, Yue Zhao <jasonzhao0307 at gmail.com>, Anthony Nicholas Federico <anfed at bu.edu>, W. Evan Johnson <wej at bu.edu>

Maintainer: Solaiappan Manimaran <manimaran_1975 at hotmail.com>, Yue Zhao <jasonzhao0307 at gmail.com>

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

Solaiappan Manimaran, Matthew Bendall, Sandro Valenzuela Diaz, Eduardo Castro, Tyler Faits, Yue Zhao, Anthony Nicholas Federico, W. Evan Johnson. PathoStat: PathoStat Statistical Microbiome Analysis Package. doi:10.18129/B9.bioc.PathoStat, R package version 1.38.0, https://bioconductor.org/packages/PathoStat.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("PathoStat")

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

Documentation

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

browseVignettes("PathoStat")

PathoStat intro	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GraphAndNetwork, ImmunoOncology, Metagenomics, Microarray, Microbiome, PatternLogic, PrincipalComponent, RNASeq, Sequencing, Software, Visualization
Version	1.38.0
In Bioconductor since	BioC 3.4 (R-3.3) (10 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
URL	https://github.com/mani2012/PathoStat
Bug Reports	https://github.com/mani2012/PathoStat/issues

Suggests	rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	PathoStat_1.38.0.tar.gz
Windows Binary (x86_64)	PathoStat_1.38.0.zip
macOS Binary (big-sur-x86_64)	PathoStat_1.38.0.tgz
macOS Binary (sonoma-arm64)	PathoStat_1.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PathoStat
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/PathoStat
Package Short Url	https://bioconductor.org/packages/PathoStat/
Package Downloads Report	Download Stats