PathoStat

DOI: 10.18129/B9.bioc.PathoStat    

PathoStat Statistical Microbiome Analysis Package

Bioconductor version: Release (3.6)

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>, W. Evan Johnson <wej at bu.edu>

Maintainer: Solaiappan Manimaran <manimaran_1975 at hotmail.com>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("PathoStat")

Documentation

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

browseVignettes("PathoStat")

 

PDF	R Script	PathoStatUserManual
HTML	R Script	PathoStatAdvanced
HTML		PathoStatIntro
PDF		Reference Manual
Text		NEWS

Details

biocViews	GraphAndNetwork, Metagenomics, Microarray, Microbiome, PatternLogic, PrincipalComponent, RNASeq, Sequencing, Software, Visualization
Version	1.4.1
In Bioconductor since	BioC 3.4 (R-3.3) (1.5 years)
License	GPL (>= 2)
Depends	R (>= 3.3.1)
Imports	MCMCpack, limma, corpcor, rmarkdown, knitr, pander, matrixStats, reshape2, scales, ggplot2, rentrez, BatchQC, DT, gtools, tidyr, plyr, dplyr, ape, phyloseq, shiny, grDevices, stats, methods, XML, graphics, utils, alluvial, BiocStyle, edgeR, preprocessCore, DESeq2
LinkingTo
Suggests	testthat
SystemRequirements	pandoc (http://pandoc.org/installing.html) for generating reports from markdown files.
Enhances
URL	https://github.com/mani2012/PathoStat
BugReports	https://github.com/mani2012/PathoStat/issues
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	PathoStat_1.4.1.tar.gz
Windows Binary	PathoStat_1.4.1.zip
Mac OS X 10.11 (El Capitan)	PathoStat_1.4.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PathoStat
Package Short Url	http://bioconductor.org/packages/PathoStat/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive