Package: lefser 1.17.1

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]

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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-1.17.0(bioc 3.21)lefser-1.16.0(bioc 3.20)

software sequencing differentialexpression microbiome statisticalmethod classification bioconductor-package

8.35 score 43 stars 59 scripts 863 downloads 8 exports 100 dependencies

Last updated 22 days agofrom:db693db070. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	WARNING	Oct 31 2024
R-4.5-linux	WARNING	Oct 31 2024
R-4.4-win	WARNING	Oct 31 2024
R-4.4-mac	WARNING	Oct 31 2024
R-4.3-win	WARNING	Oct 31 2024
R-4.3-mac	WARNING	Oct 31 2024

Exports:get_terminal_nodes lefser lefserClades lefserPlot lefserPlotClad lefserPlotFeat relativeAb rowNames2RowData

Dependencies:abind ape aplot askpass Biobase BiocGenerics brio callr cli codetools coin colorspace cpp11 crayon curl DelayedArray desc diffobj digest dplyr evaluate fansi farver forcats fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggfun ggplot2 ggplotify ggtree glue gridGraphics gtable httr IRanges isoband jsonlite labeling lattice lazyeval libcoin lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime modeltools multcomp munsell mvtnorm nlme openssl patchwork pillar pkgbuild pkgconfig pkgload praise processx ps purrr R6 RColorBrewer Rcpp rematch2 rlang rprojroot S4Arrays S4Vectors sandwich scales SparseArray stringi stringr SummarizedExperiment survival sys testthat TH.data tibble tidyr tidyselect tidytree treeio UCSC.utils utf8 vctrs viridisLite waldo withr XVector yulab.utils zlibbioc zoo

lefser: a Megatanomic biomarker discovery tool

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

Rendered fromlefser.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-09-25
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