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    64 repositories

    • fmh-funprofiler

      Public
      A functional profiler for metagenomes using FracMinHash
      Python
      •
      MIT License
      •7•21•3•2•Updated Apr 20, 2026Apr 20, 2026

    • Logan_Analyses

      Public
      Jupyter Notebook
      •0•0•5•0•Updated Apr 20, 2026Apr 20, 2026

    • dnds_using_fmh_reproducibles

      Public
      Python
      •0•1•0•0•Updated Apr 9, 2026Apr 9, 2026

    • YACHT

      Public
      A mathematically characterized hypothesis test for organism presence/absence in a metagenome
      C++
      •
      MIT License
      •10•34•15•4•Updated Mar 30, 2026Mar 30, 2026

    • branch-lengths-assignment

      Public
      Python
      •0•0•0•0•Updated Mar 29, 2026Mar 29, 2026

    • reproducing-jespersen-25

      Public
      My attempt to reproduce the paper of https://arxiv.org/abs/2503.03816
      Jupyter Notebook
      •0•0•1•0•Updated Mar 29, 2026Mar 29, 2026

    • Koslicki-lab-PSU

      Public
      Website for Koslicki Lab.
      bioinformaticscomputational-biologymetagenomics
      bioinformaticscomputational-biologymetagenomics
      HTML
      •3•0•0•0•Updated Feb 14, 2026Feb 14, 2026

    • DrugBankNER

      Public
      ETL of DrugBank to recognize KG2 concepts in DrugBank entries for use as training data
      Python
      •1•1•0•0•Updated Feb 10, 2026Feb 10, 2026

    • known_microbe_hashes

      Public
      A collection of the FMH hashes for every microbial database I can get my hands on
      Python
      •
      MIT License
      •0•1•1•2•Updated Jan 27, 2026Jan 27, 2026

    • frac-kmc

      Public
      Fast FracMinHash sketch generator
      C++
      •2•8•0•0•Updated Jan 7, 2026Jan 7, 2026

    • dnds-using-fmh

      Public
      Python
      •0•1•1•0•Updated Dec 4, 2025Dec 4, 2025

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.9k•0•0•0•Updated Dec 3, 2025Dec 3, 2025

    • MaxGeomHash

      Public
      A sub-linear sampling algorithm
      Python
      •1•1•1•0•Updated Nov 23, 2025Nov 23, 2025

    • kmer-sketch

      Public
      C++ implementation of MinHash, bottom-k MinHash, FracMinHash, MaxGeomSampling, and alpha-MaxGeomSampling
      C++
      •2•3•0•1•Updated Nov 16, 2025Nov 16, 2025

    • MetagenomicKG

      Public
      Python
      •5•18•1•0•Updated Nov 7, 2025Nov 7, 2025

    • unclassified_frequent_Logan_metagenome_hashes

      Public
      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
      •0•0•1•0•Updated Oct 14, 2025Oct 14, 2025

    • prokrustean

      Public
      C++
      •
      GNU General Public License v3.0
      •0•7•1•0•Updated Sep 20, 2025Sep 20, 2025

    • ingest_logan_yacht_data

      Public
      MVP
      Python
      •
      Apache License 2.0
      •0•0•5•1•Updated Sep 10, 2025Sep 10, 2025

    • DnDs-visualization

      Public
      A repo for the larger scale DnDs project, along with the visualization code
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 9, 2025Sep 9, 2025

    • GenBank_WGS_analysis

      Public
      Download, sketch, and enumerate unique hashes of GenBank WGS
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 18, 2025Aug 18, 2025

    • Translator_summary_guardrails

      Public
      0•0•0•0•Updated Jul 31, 2025Jul 31, 2025

    • estimate_rates_using_mutation_model

      Public
      This repository computes insertion, deletion, and substitution rates simultaneously under a non-simple mutation model using k-mers
      Python
      •1•2•0•0•Updated Jul 11, 2025Jul 11, 2025

    • est_rates_experiments

      Public
      Using simulated experiments, we will see if we can estimate the rates good enough.
      Python
      •0•0•0•0•Updated May 8, 2025May 8, 2025

    • LLMFactCheck

      Public
      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
      •0•1•10•1•Updated May 5, 2025May 5, 2025

    • .github

      Public
      Public profile
      0•0•0•0•Updated Apr 24, 2025Apr 24, 2025

    • Beta-diversity-of-mixtures-over-time

      Public
      Beta diversity of mixtures over time
      Python
      •0•0•0•0•Updated Apr 7, 2025Apr 7, 2025

    • KEGG_sketching_annotation_reproducibles

      Public
      Reproducible scripts for all KEGG + Sourmash gather computations for the associated paper
      Python
      •
      MIT License
      •0•1•1•0•Updated Mar 20, 2025Mar 20, 2025

    • fmh_cosine_reproducibles

      Public
      Reproducibility code for the manuscript "Cosine similarity using FracMinHash sketches"
      Python
      •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

    • ML-on-MKG

      Public
      Machine learning on the metagenomics knowledge graph
      Python
      •0•0•0•0•Updated Jan 16, 2025Jan 16, 2025

    • sourmash_alternate_implementations

      Public
      Implement prefetch in cpp to investigate potential speedups
      Standard ML
      •3•0•9•0•Updated Dec 23, 2024Dec 23, 2024
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