ArticleBioinformatics (Oxford, England)2024
lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Del immune V and microbiome restructuring in colorectal cancer surgery: a randomized double blind placebo controlled trial.Frontiers in cellular and infection microbiology · 2026Trial
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- Dynamic flexibility of the murine gut microbiota during morphine disturbance enables escape from the stable dysbiosis that is associated with addiction-like behavior.Gut microbes · 2026Article
- Evaluation of dietary curcumin-loaded mesoporous silica nanoparticles on growth, blood biochemistry, gut barrier integrity and enteric gas emissions in weaned piglets.Veterinary and animal science · 2026Article
- Integrative profiling of oral fungal communities acrossAnnals of medicine · 2026Article
- Insights into the dynamics of antibiotic resistance genes in the human gut microbiome across populations.Gut pathogens · 2026Article
- Lycopene mitigates T-2 toxin-induced systemic inflammation and oxidative stress in association with gut microbiota and SCFAs regulation in mice.Stress biology · 2026Article
- Inhalation of cadmium oxide nanoparticles alters intestinal and pulmonary microbiomes in mice.Applied microbiology and biotechnology · 2026Article
- Association between the oral microbiota and hyperlipidemia: evidence from a national cross-sectional study.Annals of medicine and surgery (2012) · 2026Article
- The utilization of a magneto-fluorescence sequential labeling strategy for the visualization and tracking of intestinal translocation of oral microbiota.Materials today. Bio · 2026Article
- Multi-omics integration analyses reveal microbiome and metabolome features in pregnant sow diarrhea induced by porcine epidemic diarrhea virus.BMC microbiology · 2026Article
- Metagenomic insights into viral and microbial genes of Russian High-Arctic soil microbiomes.Communications biology · 2026Article
- Amelioration of colitis through restored gut ecology using Christensenella intestinihominis AF73-05CM02 as a probiotic in mice.Communications biology · 2026Article
- Fecal microbiota transplantation plus immunotherapy in metastatic renal cell carcinoma: the phase 1 PERFORM trial.Nature medicine · 2026Article
- Developing and Evaluating Aquatic Passive Sampling of Environmental DNA for Microbial Community Profiling.Molecular ecology resources · 2026Article
- Shifts in Small Fish Community Caused by Coral Cover Variation at a Remote Reef in the South China Sea.Ecology and evolution · 2026Article
- A clinical next-generation sequencing study on the microbial profiles of asymptomatic apical periodontitis in type 2 diabetic and systemically healthy individuals following adjuvant antimicrobial photodynamic therapy.Clinical oral investigations · 2026Article
- Association between the gut microbiome and neurodevelopmental outcomes in infants with congenital heart disease: A prospective cohort study.JPEN. Journal of parenteral and enteral nutrition · 2026Article
- The study on the identification of cross-boundary microbiome enterotypes between high-altitude and coastal populations and their predictive value.BMC microbiology · 2026Article
- Relationship BetweenVeterinary sciences · 2026Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
summaryLEfSe is a widely used Python package and Galaxy module for metagenomic biomarker discovery and visualization, utilizing the Kruskal-Wallis test, Wilcoxon Rank-Sum test, and Linear Discriminant Analysis. R/Bioconductor provides a large collection of tools for metagenomic data analysis but has lacked an implementation of this widely used algorithm, hindering benchmarking against other tools and incorporation into R workflows. We present the lefser package to provide comparable functionality within the R/Bioconductor ecosystem of statistical analysis tools, with improvements to the original algorithm for performance, accuracy, and reproducibility. We benchmark the performance of lefser against the original algorithm using human and mouse metagenomic datasets. AVAILABILITY AND IMPLEMENTATION: Our software, lefser, is distributed through the Bioconductor project (https://www.bioconductor.org/packages/release/bioc/html/lefser.html), and all the source code is available in the GitHub repository https://github.com/waldronlab/lefser.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.