Package: lefser 1.23.0

Sehyun Oh

lefser: R implementation of the LEfSE method for microbiome biomarker discovery

lefser is the R implementation of the popular microbiome biomarker discovery too, LEfSe. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers from two-level classes (and optional sub-classes).

Authors:Sehyun Oh [cre, ctb], Asya Khleborodova [aut], Samuel Gamboa-Tuz [ctb], Marcel Ramos [ctb], Ludwig Geistlinger [ctb], Levi Waldron [ctb], NCI [fnd]

lefser_1.23.0.tar.gz
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lefser_1.23.0.tgz(r-4.6-any)lefser_1.23.0.tgz(r-4.5-any)
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lefser_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
lefser/json (API)

# Install 'lefser' in R:

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

Bug tracker:https://github.com/waldronlab/lefser/issues

Datasets:

zeller14 - Example dataset for lefser

On BioConductor:lefser-1.23.0(bioc 3.24)lefser-1.22.0(bioc 3.23)

software sequencing differentialexpression microbiome statisticalmethod classification bioconductor-package r01ca230551

8.55 score 66 stars 108 scripts 1.2k downloads 8 exports 171 dependencies

Last updated from:a0a8ddd4c8. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	248
linux-devel-x86_64	NOTE	453
source / vignettes	OK	298
linux-release-x86_64	NOTE	471
macos-release-arm64	NOTE	196
macos-oldrel-arm64	NOTE	194
windows-devel	NOTE	588
windows-release	NOTE	569
windows-oldrel	NOTE	499
wasm-release	OK	221

Exports:get_terminal_nodes lefser lefserClades lefserPlot lefserPlotClad lefserPlotFeat relativeAb rowNames2RowData

Dependencies:abind ape aplot assorthead base64enc beachmat beeswarm BH Biobase BiocBaseUtils BiocGenerics BiocNeighbors BiocParallel BiocSingular Biostrings bluster brio bslib cachem Cairo callr cli cluster codetools coin cpp11 crayon DBI DECIPHER decontam DelayedArray DelayedMatrixStats desc diffobj digest DirichletMultinomial dplyr dqrng ecodive evaluate farver fastmap FNN fontawesome fontBitstreamVera fontLiberation fontquiver forcats formatR fs futile.logger futile.options gdtools generics GenomicRanges ggbeeswarm ggfun ggiraph ggplot2 ggplotify ggrastr ggrepel ggtree glue gridExtra gridGraphics gtable highr htmltools htmlwidgets igraph IRanges irlba isoband jquerylib jsonlite knitr labeling lambda.r lattice lazyeval libcoin lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mia mime modeltools multcomp MultiAssayExperiment mvtnorm nlme otel patchwork permute pheatmap pillar pkgbuild pkgconfig pkgload plyr png praise processx ps purrr R6 ragg rappdirs RColorBrewer Rcpp RcppAnnoy RcppEigen RcppML RcppProgress reshape2 rlang rmarkdown rprojroot RSpectra rsvd Rtsne S4Arrays S4Vectors S7 sandwich sass ScaledMatrix scales scater scuttle Seqinfo SingleCellExperiment sitmo snow SparseArray sparseMatrixStats stringi stringr SummarizedExperiment survival systemfonts testthat textshaping TH.data tibble tidyr tidyselect tidytree tinytex treeio TreeSummarizedExperiment utf8 uwot vctrs vegan vipor viridis viridisLite waldo withr xfun XVector yaml yulab.utils zoo

lefser: a metagenomic biomarker discovery tool

Rendered fromlefser.Rmdusingknitr::rmarkdown

Last update: 2025-11-07
Started: 2020-07-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Identify which elements of a string are terminal nodes	get_terminal_nodes
R implementation of the LEfSe method	lefser
Run lefser at different clades	lefserClades
Plots results from 'lefser' function	lefserPlot
LEfSer plot cladogram	lefserPlotClad
Plot Feature	lefserPlotFeat
Utility function to calculate relative abundances	relativeAb
RowNames to RowData	rowNames2RowData
Example dataset for lefser	zeller14