PathoStat

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see PathoStat.

PathoStat Statistical Microbiome Analysis Package

Bioconductor version: 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>

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

Installation

To install this package, start R (version "3.4") 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")

PathoStatUserManual	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

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) (7.5 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
System Requirements	pandoc (http://pandoc.org/installing.html) for generating reports from markdown files.
URL	https://github.com/mani2012/PathoStat
Bug Reports	https://github.com/mani2012/PathoStat/issues

Suggests	testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report	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
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
Old Source Packages for BioC 3.6	Source Archive