Package: LegATo 1.6.0

Aubrey Odom

LegATo: LegATo: Longitudinal mEtaGenomic Analysis Toolkit

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.

Authors:Aubrey Odom [aut, cre], Yilong Zhang [ctb], Jared Pincus [csl], Jordan Pincus [art]

LegATo_1.6.0.tar.gz
LegATo_1.6.0.tar.gz(r-4.7-any)LegATo_1.6.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
LegATo/json (API)

# Install 'LegATo' in R:

install.packages('LegATo', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/wejlab/legato/issues

Pkgdown/docs site:https://wejlab.github.io

On BioConductor:LegATo-1.7.0(data/experiment 3.24)LegATo-1.6.0(data/experiment 3.23)

microbiomedata reproducibleresearch sequencingdata analysis bioconductor bioinformatics longitudinal metagenomics microbiome datapkg

4.60 score 2 stars 10 scripts 21 exports 180 dependencies

Last updated from:b9eabb97eb (on RELEASE_3_23). Checks:1 NOTE, 3 OK. Indexed: no.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	NOTE	303
linux-devel	OK	436
source / vignettes	OK	408
linux-release	OK	452

Exports:clean_MAE create_formatted_MAE distinctColors filter_animalcules_MAE filter_MAE get_long_data get_stacked_data get_summary_table get_top_taxa NMIT parse_MAE_SE plot_alluvial plot_heatmap plot_spaghetti plot_stacked_area plot_stacked_bar run_gee_model run_lm_model run_lmm_model test_hotelling_t2 tscor

Dependencies:abind animalcules ape askpass assertthat base64enc BH Biobase BiocBaseUtils BiocGenerics BiocParallel bslib cachem caret class cli clock clue cluster codetools commonmark covr cpp11 crosstalk curl data.table DelayedArray DESeq2 diagram digest dirmult dplyr DT e1071 evaluate farver fastmap fBasics fontawesome forcats foreach formatR fs futile.logger futile.options future future.apply generics GenomicRanges ggforce ggplot2 ggrepel globals glue gower gss gtable GUniFrac hardhat here highr htmltools htmlwidgets httpuv httr inline ipred IRanges isoband iterators jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lava lazyeval lifecycle limma listenv locfit lubridate magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime modeest ModelMetrics MultiAssayExperiment nlme nnet numDeriv openssl otel parallelly permute pillar pkgconfig plotly plyr png polyclip pROC prodlim progressr promises proxy purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RcppTOML recipes rentrez reshape2 reticulate rex rlang rmarkdown rmutil ROCit rpart rprojroot RSpectra S4Arrays S4Vectors S7 sass scales Seqinfo shape shiny shinyjs snow sourcetools SparseArray sparsevctrs spatial SQUAREM stable stabledist statip statmod stringi stringr SummarizedExperiment survival sys systemfonts tibble tidyr tidyselect timechange timeDate timeSeries tinytex tsne tweenr tzdb umap utf8 vctrs vegan viridisLite withr xfun XML xtable XVector yaml

LegATo Tutorial

Rendered fromLegATo_vignette.Rmdusingknitr::rmarkdown

Last update: 2025-04-07
Started: 2024-01-23

Help page	Topics
Clean up taxon names in a MultiAssayExperiment	clean_MAE
Create a formatted MultiAssayExperiment compatible with LegATo	create_formatted_MAE
Generate a distinct palette for coloring different clusters.	distinctColors
Filter a MultiAssayExperiment to a top percentage of taxa and label the rest as "Other"	filter_animalcules_MAE
Filter a MultiAssayExperiment object to keep a top percentage of taxa	filter_MAE
Create a long data.frame from a MultiAssayExperiment counts object	get_long_data
Create a long data.frame with grouped abundances from a MultiAssayExperiment counts object	get_stacked_data
Create a table summarizing reads aggregated by grouping variables on a unit	get_summary_table
Obtain a data.frame of ordered taxa abundances at a given level	get_top_taxa
Nonparametric Microbial Interdependence Test (NMIT)	NMIT
Parse a MultiExperimentAssay object and extract the elements as data.frames	parse_MAE_SE
Plot an alluvial diagram of microbial relative abundance	plot_alluvial
Plot a ComplexHeatmap.	plot_heatmap
Plot a spaghetti volatility plot of microbial abundance for a given taxon	plot_spaghetti
Plot a stacked area chart of microbial relative abundance	plot_stacked_area
Plot a stacked bar chart of microbial relative abundance	plot_stacked_bar
Compute Generalized Estimating Equations (GEEs) on longitudinal microbiome data	run_gee_model
Compute linear models (LM) on microbiome data	run_lm_model
Compute linear mixed-effects models (LMM) on longitudinal microbiome data	run_lmm_model
Conduct a multivariate Hotelling's T-squared test	test_hotelling_t2
Calculate within-subject OTU correlations	tscor

Package: LegATo 1.6.0

LegATo: LegATo: Longitudinal mEtaGenomic Analysis Toolkit

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)