metagenomeSeq
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see metagenomeSeq.
Statistical analysis for sparse high-throughput sequencing
Bioconductor version: 3.16
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 <jpaulson at jimmy.harvard.edu>
citation("metagenomeSeq")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | R Script | |
| metagenomeSeq: statistical analysis for sparse high-throughput sequencing | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Clustering, DifferentialExpression, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software, Visualization |
| Version | 1.40.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (11 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 | etec16s, metavizr, microbiomeExplorer, msd16s |
| Imports Me | benchdamic, Maaslin2, microbiomeDASim, microbiomeMarker |
| Suggests Me | interactiveDisplay, phyloseq, scTreeViz, Wrench |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | metagenomeSeq_1.40.0.tar.gz |
| Windows Binary | metagenomeSeq_1.40.0.zip |
| macOS Binary (x86_64) | metagenomeSeq_1.40.0.tgz |
| macOS Binary (arm64) | metagenomeSeq_1.40.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/metagenomeSeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/metagenomeSeq |
| Bioc Package Browser | https://code.bioconductor.org/browse/metagenomeSeq/ |
| Package Short Url | https://bioconductor.org/packages/metagenomeSeq/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |