Registration and Call for Abstracts Open for Bioc2024

PathoStat

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

PathoStat Statistical Microbiome Analysis Package


Bioconductor version: Development (3.19)

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews GraphAndNetwork, ImmunoOncology, Metagenomics, Microarray, Microbiome, PatternLogic, PrincipalComponent, RNASeq, Sequencing, Software, Visualization
Version 1.29.0
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_1.29.0.tar.gz
Windows Binary PathoStat_1.29.0.zip
macOS Binary (x86_64) PathoStat_1.29.0.tgz
macOS Binary (arm64) PathoStat_1.29.0.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