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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 (3.6)

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>, Matthew Bendall <bendall at>, Sandro Valenzuela Diaz <sandrolvalenzuelad at>, Eduardo Castro <castronallar at>, Tyler Faits <tfaits at>, W. Evan Johnson <wej at>

Maintainer: Solaiappan Manimaran <manimaran_1975 at>

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


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PDF R Script PathoStatUserManual
HTML R Script PathoStatAdvanced
HTML PathoStatIntro
PDF   Reference Manual
Text   NEWS


biocViews GraphAndNetwork, Metagenomics, Microarray, Microbiome, PatternLogic, PrincipalComponent, RNASeq, Sequencing, Software, Visualization
Version 1.3.0
In Bioconductor since BioC 3.4 (R-3.3) (1 year)
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
Suggests testthat
SystemRequirements pandoc ( for generating reports from markdown files.
Depends On Me
Imports Me
Suggests Me
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