PathoStat

DOI: 10.18129/B9.bioc.PathoStat    

This is the development version of PathoStat; for the stable release version, see PathoStat.

PathoStat Statistical Microbiome Analysis Package

Bioconductor version: Development (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>, 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")):

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

HTML R Script PathoStat intro
PDF   Reference Manual
Text   NEWS

Details

biocViews GraphAndNetwork, Metagenomics, Microarray, Microbiome, PatternLogic, PrincipalComponent, RNASeq, Sequencing, Software, Visualization
Version 1.7.0
In Bioconductor since BioC 3.4 (R-3.3) (1.5 years)
License GPL (>= 2)
Depends R (>= 3.4)
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
Build Report  

Package Archives

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

Source Package PathoStat_1.7.0.tar.gz
Windows Binary PathoStat_1.7.0.zip
Mac OS X 10.11 (El Capitan) PathoStat_1.7.0.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 http://bioconductor.org/packages/PathoStat/
Package Downloads Report Download Stats

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