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

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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/

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Old Source Packages for BioC 3.6 Source Archive