Package: lefser 1.17.6

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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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:

On BioConductor:lefser-1.17.4(bioc 3.21)lefser-1.16.0(bioc 3.20)

softwaresequencingdifferentialexpressionmicrobiomestatisticalmethodclassificationbioconductor-package

8.47 score 55 stars 56 scripts 913 downloads 8 exports 183 dependencies

Last updated 1 days agofrom:2138c66772. Checks:1 OK, 7 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 19 2025
R-4.5-winWARNINGFeb 19 2025
R-4.5-macWARNINGFeb 19 2025
R-4.5-linuxWARNINGFeb 19 2025
R-4.4-winWARNINGFeb 19 2025
R-4.4-macWARNINGFeb 19 2025
R-4.3-winWARNINGFeb 19 2025
R-4.3-macWARNINGFeb 19 2025

Exports:get_terminal_nodeslefserlefserCladeslefserPlotlefserPlotCladlefserPlotFeatrelativeAbrowNames2RowData

Dependencies:abindapeaplotaskpassassortheadbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocNeighborsBiocParallelBiocSingularBiostringsbitbit64blusterbrioCairocallrcellrangerclicliprclustercodetoolscoincolorspacecommonmarkcpp11crayoncurlDBIDECIPHERdecontamDelayedArrayDelayedMatrixStatsdescdiffobjdigestDirichletMultinomialdplyrdqrngemmeansestimabilityevaluatefansifarverfillpatternFNNforcatsformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggfunggnewscaleggplot2ggplotifyggrastrggrepelggtextggtreegluegridExtragridGraphicsgridtextgtablehmshttrigraphIRangesirlbaisobandjpegjsonlitelabelinglambda.rlatticelazyevallibcoinlifecyclemagrittrmarkdownMASSMatrixMatrixGenericsmatrixStatsmgcvmiamimemodeltoolsmultcompMultiAssayExperimentmunsellmvtnormnlmenumDerivopensslparallellypatchworkpermutepheatmappillarpkgbuildpkgconfigpkgloadplyrpngpraiseprettyunitsprocessxprogresspspurrrR6raggrbiomRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressreadrreadxlrematchreshape2rlangrprojrootRSpectrarsvdRtsneS4ArraysS4VectorssandwichScaledMatrixscalesscaterscuttleSingleCellExperimentsitmoslamsnowSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsurvivalsyssystemfontstestthattextshapingTH.datatibbletidyrtidyselecttidytreetreeioTreeSummarizedExperimenttzdbUCSC.utilsutf8uwotvctrsveganviporviridisviridisLitevroomwaldowithrxfunxml2XVectoryulab.utilszoo

lefser: a metagenomic biomarker discovery tool

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

Rendered fromlefser.Rmdusingknitr::rmarkdownon Feb 19 2025.

Last update: 2025-02-18
Started: 2020-07-23