LegATo
This is thereleased version of LegATo; for the devel version, seeLegATo.
LegATo: Longitudinal mEtaGenomic Analysis Toolkit
Bioconductor version: Release (3.22)
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: 0000-0001-7113-7598, Yilong Zhang [ctb] (Author of NMIT functions), Jared Pincus [csl] (ORCID: ORCID: 0000-0001-6708-5262, other: Naming consultant of package), Jordan Pincus [art] (Artist of LegATo icon)
Maintainer: Aubrey Odom <aodom at bu.edu>
citation("LegATo")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("LegATo")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ExperimentData,MicrobiomeData,ReproducibleResearch,SequencingData |
| Version | 1.4.0 |
| License | MIT + fileLICENSE |
| 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 |
See More
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | LegATo_1.4.0.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 |