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("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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
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 |
See More
| Suggests | testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| 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 |