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Bioconductor - metagenomeSeq (development version)

metagenomeSeq

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

Statistical analysis for sparse high-throughput sequencing

Bioconductor version: Development (3.22)

metagenomeSeq is designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. metagenomeSeq is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.

Author: Joseph Nathaniel Paulson, Nathan D. Olson, Domenick J. Braccia, Justin Wagner, Hisham Talukder, Mihai Pop, Hector Corrada Bravo

Maintainer: Joseph N. Paulson <josephpaulson at gmail.com>

Citation (from within R, enter citation("metagenomeSeq")): Installation

To install this package, start R (version "4.5") and enter:


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

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

BiocManager::install("metagenomeSeq")

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("metagenomeSeq")
fitTimeSeries: differential abundance analysis through time or location PDF R Script metagenomeSeq: statistical analysis for sparse high-throughput sequencing PDF R Script Reference Manual PDF NEWS Text Details biocViews Classification, Clustering, DifferentialExpression, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software, Visualization Version 1.51.0 In Bioconductor since BioC 2.12 (R-3.0) (12.5 years) License Artistic-2.0 Depends R (>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer Imports parallel, matrixStats, foreach, Matrix, gplots, graphics, grDevices, stats, utils, Wrench System Requirements URL https://github.com/nosson/metagenomeSeq/ Bug Reports https://github.com/nosson/metagenomeSeq/issues See More Suggests annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay, IHW Linking To Enhances Depends On Me microbiomeExplorer, etec16s Imports Me Maaslin2, mbQTL, microbiomeDASim Suggests Me dar, interactiveDisplay, phyloseq, scTreeViz, Wrench, ggpicrust2 Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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