R implementation of the LEfSe method
☆64Nov 17, 2025Updated 4 months ago
Alternatives and similar repositories for lefser
Users that are interested in lefser are comparing it to the libraries listed below
Sorting:
- R package for microbiome biomarker discovery☆194Feb 19, 2025Updated last year
- This is the supplementary code for CRC-multi-kingdom☆17Nov 8, 2021Updated 4 years ago
- Methods used in the article "Assessment of statistical methods from single cell, bulk RNA-seq and metagenomics applied to microbiome data…☆10Jul 13, 2020Updated 5 years ago
- A comprehensive R package for deep mining microbiome☆191Nov 3, 2025Updated 4 months ago
- An R package for downstream data analysis of microbiome omics data☆272Updated this week
- Professional Comprehensive Omics Data Analysis☆32Feb 10, 2026Updated last month
- This repository includes the code used in our multiomics BMI study.☆20Jul 6, 2023Updated 2 years ago
- ☆87May 22, 2024Updated last year
- ☆19Nov 11, 2024Updated last year
- ☆15Mar 14, 2023Updated 3 years ago
- Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat☆47Feb 3, 2026Updated last month
- ☆18Jan 14, 2024Updated 2 years ago
- Ying's tools for analysis, with particular focus on microbiome data☆41Jan 27, 2026Updated last month
- MaAsLin2: Microbiome Multivariate Association with Linear Models☆152Feb 5, 2026Updated last month
- A healthy human gut genome collection☆25Aug 21, 2025Updated 7 months ago
- Pipeline for metabolic annotation of microbial genomes☆150Mar 20, 2025Updated last year
- A shiny package for microbiome functional enrichment analysis☆38Dec 23, 2025Updated 2 months ago
- ☆58Mar 14, 2024Updated 2 years ago
- gutSMASH☆58Oct 3, 2025Updated 5 months ago
- KEGG Module Evaluation Tool☆33Mar 5, 2026Updated 2 weeks ago
- Analyze a set of genomes with the anvi'o pangenome pipeline☆16Oct 11, 2023Updated 2 years ago
- Import qiime2 artifacts to R☆176Dec 12, 2024Updated last year
- ISCompare, an opensource program to identify Differentially Located Insertion Sequences☆14Jul 30, 2024Updated last year
- KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files☆370Aug 1, 2025Updated 7 months ago
- Microbial marker identification from cross-cohort datasets☆14May 15, 2024Updated last year
- Make Picrust2 Output Analysis and Visualization Easier☆186Feb 12, 2026Updated last month
- bioBakery tools for meta'omic profiling☆309Jun 3, 2025Updated 9 months ago
- Code, unit tests, and tutorials for running PICRUSt2☆384Nov 27, 2025Updated 3 months ago
- Hybrid Assembler for Plasmids☆10Jul 28, 2022Updated 3 years ago
- A comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.☆28Feb 14, 2023Updated 3 years ago
- ☆18Oct 13, 2023Updated 2 years ago
- Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data☆170Sep 4, 2025Updated 6 months ago
- Dynamic Multivariate Data Analysis and Visualization Platform☆41Nov 8, 2015Updated 10 years ago
- R package for computing alpha and beta contributional diversity metrics☆11May 5, 2023Updated 2 years ago
- This is the source code for ARGs-OAP v2.0 construction☆12Aug 1, 2019Updated 6 years ago
- Unified Human Gut Virome Catalog☆41Nov 10, 2025Updated 4 months ago
- The viral taxonomic assignment pipeline☆43Feb 5, 2026Updated last month
- Pipeline for identification of eukaryotic contigs in metagenomic assemblies☆13Mar 14, 2024Updated 2 years ago
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆21Mar 1, 2026Updated 2 weeks ago