PathoStat

DOI: 10.18129/B9.bioc.PathoStat    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see PathoStat.

PathoStat Statistical Microbiome Analysis Package

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

HTML	R Script	PathoStat intro
PDF		Reference Manual
Text		NEWS

Details

biocViews	GraphAndNetwork, ImmunoOncology, Metagenomics, Microarray, Microbiome, PatternLogic, PrincipalComponent, RNASeq, Sequencing, Software, Visualization
Version	1.8.4
In Bioconductor since	BioC 3.4 (R-3.3) (2.5 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
LinkingTo
Suggests	rmarkdown, testthat
SystemRequirements
Enhances
URL	https://github.com/mani2012/PathoStat
BugReports	https://github.com/mani2012/PathoStat/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	PathoStat_1.8.4.tar.gz
Windows Binary	PathoStat_1.8.4.zip
Mac OS X 10.11 (El Capitan)	PathoStat_1.8.4.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	http://bioconductor.org/packages/PathoStat/
Package Downloads Report	Download Stats