☆87May 22, 2024Updated last year
Alternatives and similar repositories for lefse
Users that are interested in lefse are comparing it to the libraries listed below
Sorting:
- ISCompare, an opensource program to identify Differentially Located Insertion Sequences☆14Jul 30, 2024Updated last year
- bioBakery tools for meta'omic profiling☆305Jun 3, 2025Updated 8 months ago
- Ying's tools for analysis, with particular focus on microbiome data☆41Jan 27, 2026Updated last month
- R implementation of the LEfSe method☆63Nov 17, 2025Updated 3 months ago
- HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).☆235Jan 20, 2026Updated last month
- Precise phylogenetic analysis of microbial isolates and genomes from metagenomes☆160Feb 13, 2026Updated 2 weeks ago
- MaAsLin2: Microbiome Multivariate Association with Linear Models☆153Feb 5, 2026Updated 3 weeks ago
- Code, unit tests, and tutorials for running PICRUSt2☆381Nov 27, 2025Updated 3 months ago
- KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files☆366Aug 1, 2025Updated 6 months ago
- Hybrid Assembler for Plasmids☆10Jul 28, 2022Updated 3 years ago
- Conversion software tool for producing both annotation and tree files for GraPhlAn☆11Feb 2, 2022Updated 4 years ago
- ☆19Dec 4, 2025Updated 2 months ago
- A Python package for microbiome sequencing analysis with QIIME 2☆47Jan 28, 2024Updated 2 years ago
- A Linear Discriminant Analysis Effect Size (LEfSe) wrapper.☆26Feb 2, 2017Updated 9 years ago
- Differential abundance (DA) and correlation analyses for microbial absolute abundance data☆130Sep 5, 2025Updated 5 months ago
- CLI tool to annotate genes with KOfam☆89Jun 6, 2023Updated 2 years ago
- A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations☆44Apr 4, 2023Updated 2 years ago
- Visualize microbiome data with black magic ggtree☆68Sep 3, 2020Updated 5 years ago
- MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data☆393Dec 13, 2025Updated 2 months ago
- Download assembly files from NCBI☆13May 9, 2023Updated 2 years ago
- some useful scripts for working with genomics and sequencing data☆17Oct 31, 2019Updated 6 years ago
- Metagenome analysis pipeline☆100Jul 26, 2021Updated 4 years ago
- High-quality circular representations of taxonomic and phylogenetic trees☆106Aug 7, 2024Updated last year
- Microbial ecological network visualization clustering☆144Nov 20, 2025Updated 3 months ago
- This is the supplementary code for CRC-multi-kingdom☆17Nov 8, 2021Updated 4 years ago
- bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validate…☆129Oct 20, 2025Updated 4 months ago
- R package for microbiome biomarker discovery☆193Feb 19, 2025Updated last year
- Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…☆402Jan 12, 2026Updated last month
- 16S rRNA marker gene upstream and dowstream analysis tutorial for the UCT Hex cluster.☆11Jan 15, 2021Updated 5 years ago
- An R interface to the omixer-rpm for turning metagenomic functional profiles into pathway/module profiles☆12Dec 16, 2022Updated 3 years ago
- Ontology-aware neural network (ONN) for microbial community sample source tracking!☆10Oct 11, 2022Updated 3 years ago
- GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.☆580Feb 21, 2026Updated last week
- An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.☆49Apr 20, 2023Updated 2 years ago
- Profiler for metagenomics based on NGLess☆13Feb 22, 2024Updated 2 years ago
- Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for…☆160Apr 23, 2025Updated 10 months ago
- Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.☆143Dec 17, 2025Updated 2 months ago
- A companion R package for the MicrobiomeAnalyst web server☆131Updated this week
- Sparse InversE Covariance estimation for Ecological Association and Statistical Inference☆229Oct 29, 2025Updated 4 months ago
- KEGG Module Evaluation Tool☆32Nov 15, 2023Updated 2 years ago