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    • A functional profiler for metagenomes using FracMinHash
      Python
      MIT License
      72132Updated Apr 20, 2026Apr 20, 2026
    • Jupyter Notebook
      0050Updated Apr 20, 2026Apr 20, 2026
    • Python
      0100Updated Apr 9, 2026Apr 9, 2026
    • YACHT

      Public
      A mathematically characterized hypothesis test for organism presence/absence in a metagenome
      C++
      MIT License
      1034154Updated Mar 30, 2026Mar 30, 2026
    • Python
      0000Updated Mar 29, 2026Mar 29, 2026
    • My attempt to reproduce the paper of https://arxiv.org/abs/2503.03816
      Jupyter Notebook
      0010Updated Mar 29, 2026Mar 29, 2026
    • Website for Koslicki Lab.
      HTML
      3000Updated Feb 14, 2026Feb 14, 2026
    • ETL of DrugBank to recognize KG2 concepts in DrugBank entries for use as training data
      Python
      1100Updated Feb 10, 2026Feb 10, 2026
    • A collection of the FMH hashes for every microbial database I can get my hands on
      Python
      MIT License
      0112Updated Jan 27, 2026Jan 27, 2026
    • frac-kmc

      Public
      Fast FracMinHash sketch generator
      C++
      2800Updated Jan 7, 2026Jan 7, 2026
    • Python
      0110Updated Dec 4, 2025Dec 4, 2025
    • Conda recipes for the bioconda channel.
      Shell
      MIT License
      3.9k000Updated Dec 3, 2025Dec 3, 2025
    • A sub-linear sampling algorithm
      Python
      1110Updated Nov 23, 2025Nov 23, 2025
    • C++ implementation of MinHash, bottom-k MinHash, FracMinHash, MaxGeomSampling, and alpha-MaxGeomSampling
      C++
      2301Updated Nov 16, 2025Nov 16, 2025
    • Python
      51810Updated Nov 7, 2025Nov 7, 2025
    • The goal will be to obtain a shortlist of hashes that show up in lots of metagenomes, but aren't classified in any databases like GTDB, GenBank WGS, BLAST nr, e…
      Python
      MIT License
      0010Updated Oct 14, 2025Oct 14, 2025
    • C++
      GNU General Public License v3.0
      0710Updated Sep 20, 2025Sep 20, 2025
    • MVP
      Python
      Apache License 2.0
      0051Updated Sep 10, 2025Sep 10, 2025
    • A repo for the larger scale DnDs project, along with the visualization code
      Jupyter Notebook
      MIT License
      0000Updated Sep 9, 2025Sep 9, 2025
    • Download, sketch, and enumerate unique hashes of GenBank WGS
      Python
      MIT License
      0000Updated Aug 18, 2025Aug 18, 2025
    • 0000Updated Jul 31, 2025Jul 31, 2025
    • This repository computes insertion, deletion, and substitution rates simultaneously under a non-simple mutation model using k-mers
      Python
      1200Updated Jul 11, 2025Jul 11, 2025
    • Using simulated experiments, we will see if we can estimate the rates good enough.
      Python
      0000Updated May 8, 2025May 8, 2025
    • The "LLMFactCheck" is a powerful tool designed to semantic triples (subject–predicate–object) in different sources, ensuring the accuracy of references and enha…
      Python
      MIT License
      01101Updated May 5, 2025May 5, 2025
    • .github

      Public
      Public profile
      0000Updated Apr 24, 2025Apr 24, 2025
    • Beta diversity of mixtures over time
      Python
      0000Updated Apr 7, 2025Apr 7, 2025
    • Reproducible scripts for all KEGG + Sourmash gather computations for the associated paper
      Python
      MIT License
      0110Updated Mar 20, 2025Mar 20, 2025
    • Reproducibility code for the manuscript "Cosine similarity using FracMinHash sketches"
      Python
      0000Updated Jan 30, 2025Jan 30, 2025
    • ML-on-MKG

      Public
      Machine learning on the metagenomics knowledge graph
      Python
      0000Updated Jan 16, 2025Jan 16, 2025
    • Implement prefetch in cpp to investigate potential speedups
      Standard ML
      3090Updated Dec 23, 2024Dec 23, 2024
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