Skip to content
Optimal Microbiome-based Association Test (OMiAT)
R
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
R
data
man
DESCRIPTION
NAMESPACE
OMiAT-manual.pdf
OMiAT_5.3.tar.gz
README.md

README.md

R package: OMiAT

Version: 5.3

Date: 2017-6-13

Title: Optimal Microbiome-based Association Test (OMiAT)

Author: Hyunwook Koh, Martin J. Blaser, and Huilin Li

Maintainer: Hyunwook Koh hk1785@nyu.edu

Description: This software package provides facilities for 1) optimal microbiome-based association test (OMiAT) which tests the association for microbial community composition and 2) microbiome comprehensive association mapping (MiCAM) which tests the association for microbial composition in all different microbial taxa through a breadth of taxonomic levels (e.g., kingdom, phylum, class, order, family, genus and species). Continuous or binary traits (for either human health/disease outcomes or medical interventions) can be surveyed with/without covariate adjustments (e.g., age, sex).

NeedsCompilation: No

Depends: R(>= 3.2.3)

Imports: ape, BiasedUrn, cluster, CompQuadForm, dirmult, dummies, ecodist, GUniFrac, phangorn, phyloseq, robustbase, robCompositions

License: GPL-2

Reference

  • Koh H, Blaser MJ, Li H. (2017) A powerful microbiome-based association test and a microbial taxa discovery framework for comprehensive association mapping. Microbiome 5:45.

  • DOI: https://doi.org/10.1186/s40168-017-0262-x

Installation

library(devtools)
install_github("hk1785/OMiAT", force=T)

Data format

library(phyloseq)
You can’t perform that action at this time.