PathoStat
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see PathoStat.
PathoStat Statistical Microbiome Analysis Package
Bioconductor version: 3.9
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>, Anthony Nicholas Federico <anfed at bu.edu>, W. Evan Johnson <wej at bu.edu>
Maintainer: Solaiappan Manimaran <manimaran_1975 at hotmail.com>, Yue Zhao <jasonzhao0307 at gmail.com>
citation("PathoStat")):
Installation
To install this package, start R (version "3.6") 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")| PathoStat intro | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GraphAndNetwork, ImmunoOncology, Metagenomics, Microarray, Microbiome, PatternLogic, PrincipalComponent, RNASeq, Sequencing, Software, Visualization |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.5) |
| 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 |
| System Requirements | |
| URL | https://github.com/mani2012/PathoStat |
| Bug Reports | https://github.com/mani2012/PathoStat/issues |
See More
| Suggests | rmarkdown, 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_1.10.0.tar.gz |
| Windows Binary | PathoStat_1.10.0.zip |
| Mac OS X 10.11 (El Capitan) | PathoStat_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/PathoStat |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/PathoStat |
| Bioc Package Browser | https://code.bioconductor.org/browse/PathoStat/ |
| Package Short Url | https://bioconductor.org/packages/PathoStat/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |