PathoStat
PathoStat Statistical Microbiome Analysis Package
Bioconductor version: 3.23 · Package version: 1.38.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("PathoStat")Details
| Maintainer | Solaiappan Manimaran <manimaran_1975@hotmail.com>, Yue Zhao <jasonzhao0307@gmail.com> |
| Author | Solaiappan Manimaran <manimaran_1975@hotmail.com>, Matthew Bendall <bendall@gwmail.gwu.edu>, Sandro Valenzuela Diaz <sandrolvalenzuelad@gmail.com>, Eduardo Castro <castronallar@gmail.com>, Tyler Faits <tfaits@gmail.com>, Yue Zhao <jasonzhao0307@gmail.com>, Anthony Nicholas Federico <anfed@bu.edu>, W. Evan Johnson <wej@bu.edu> |
| License | GPL (>= 2) |
| URL | https://github.com/mani2012/PathoStat |
| Bug Reports | https://github.com/mani2012/PathoStat/issues |
| Downloads rank | 517 |
| Source branch | RELEASE_3_23 |
| biocViews | GraphAndNetwork, ImmunoOncology, Metagenomics, Microarray, Microbiome, PatternLogic, PrincipalComponent, RNASeq, Sequencing, Software, Visualization |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | PathoStat_1.38.0.tar.gz |
| Windows binary (x86_64) | PathoStat_1.38.0.zip |
| macOS binary (arm64) | PathoStat_1.38.0.tgz |
| macOS binary (x86_64) | PathoStat_1.38.0.tgz |
Dependencies
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