LegATo

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

LegATo: Longitudinal mEtaGenomic Analysis Toolkit

Bioconductor version: Development (3.21)

LegATo is a suite of open-source software tools for longitudinal microbiome analysis. It is extendable to several different study forms with optimal ease-of-use for researchers. Microbiome time-series data presents distinct challenges including complex covariate dependencies and variety of longitudinal study designs. This toolkit will allow researchers to determine which microbial taxa are affected over time by perturbations such as onset of disease or lifestyle choices, and to predict the effects of these perturbations over time, including changes in composition or stability of commensal bacteria.

Author: Aubrey Odom [aut, cre] (ORCID: ), Yilong Zhang [ctb] (Author of NMIT functions), Jared Pincus [csl] (ORCID: , other: Naming consultant of package), Jordan Pincus [art] (Artist of LegATo icon)

Maintainer: Aubrey Odom <aodom at bu.edu>

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

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("LegATo")

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("LegATo")

LegATo Tutorial	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, MicrobiomeData, ReproducibleResearch, SequencingData
Version	0.99.11
License	MIT + file LICENSE
Depends	R (>= 4.4.0)
Imports	animalcules, data.table, dplyr, ggplot2, magrittr, MultiAssayExperiment, plyr, rlang, S4Vectors, stringr, SummarizedExperiment, tibble, tidyr, tidyselect
System Requirements
URL	https://wejlab.github.io/LegATo-docs/
Bug Reports	https://github.com/wejlab/LegATo/issues

Suggests	BiocStyle, broom, broom.mixed, circlize, ComplexHeatmap, emmeans, geepack, ggalluvial, ggeffects, grDevices, knitr, lme4, lmerTest, methods, RColorBrewer, rmarkdown, spelling, TBSignatureProfiler, testthat (>= 3.0.0), TreeSummarizedExperiment, usethis, vegan
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	LegATo_0.99.11.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/LegATo
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/LegATo
Package Short Url	https://bioconductor.org/packages/LegATo/
Package Downloads Report	Download Stats