Package: lefser 1.15.3

Sehyun Oh

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

lefser is an implementation in R of the popular "LDA Effect Size (LEfSe)" method for microbiome biomarker discovery. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers of groups and sub-groups.

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

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lefser.pdf |lefser.html✨
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NEWS

# 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-1.15.0(bioc 3.20)lefser-1.14.0(bioc 3.19)

bioconductor-package

4 exports 2.00 score 82 dependencies

Last updated 8 days agofrom:c4bbf22826

Exports:get_terminal_nodes lefser lefserPlot relativeAb

Dependencies:abind askpass Biobase BiocGenerics brio callr cli codetools coin colorspace crayon curl DelayedArray desc diffobj digest dplyr evaluate fansi farver fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lattice libcoin lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime modeltools multcomp munsell mvtnorm nlme openssl pillar pkgbuild pkgconfig pkgload praise processx ps R6 RColorBrewer rematch2 rlang rprojroot S4Arrays S4Vectors sandwich scales SparseArray SummarizedExperiment survival sys testthat TH.data tibble tidyselect UCSC.utils utf8 vctrs viridisLite waldo withr XVector zlibbioc zoo

lefser: a Megatanomic biomarker discovery tool

Asya Khleborodova, Sehyun Oh, Ludwig Geistlinger, and Levi Waldron

Rendered fromlefser.Rmdusingknitr::rmarkdownon Jul 03 2024.

Last update: 2024-06-26
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
Plots results from 'lefser' function	lefserPlot
Utility function to calculate relative abundances	relativeAb
Example dataset for lefser	zeller14