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@treangenlab

Treangen Lab

Treangen Lab @ Rice University

Popular repositories Loading

  1. emu emu Public

    Python 98 15

  2. methphaser methphaser Public

    MethPhaser: methylation-based haplotype phasing of human genomes

    Python 56 6

  3. bronko bronko Public

    Ultra-rapid detection of viral variants directly from sequencing data

    Rust 47

  4. Olivar Olivar Public

    Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens

    Python 42 3

  5. lemur lemur Public

    Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets

    Python 25 1

  6. Seqwin Seqwin Public

    Ultrafast identification of signature sequences in microbial genomes

    Python 20 1

Repositories

Showing 10 of 30 repositories
  • Seqwin Public

    Ultrafast identification of signature sequences in microbial genomes

    treangenlab/Seqwin's past year of commit activity
    Python 20 GPL-3.0 1 1 0 Updated Sep 6, 2026
  • PlasmidScreen Public
    treangenlab/PlasmidScreen's past year of commit activity
    Python 1 MIT 0 2 0 Updated Sep 4, 2026
  • bronko Public

    Ultra-rapid detection of viral variants directly from sequencing data

    treangenlab/bronko's past year of commit activity
    Rust 47 MIT 0 0 0 Updated Aug 31, 2026
  • mbcausal Public

    causal inference from longitudinal gut microbiome profiles: interpretable NMF factors, an identifiability screen that runs before any effect is fit, and lagged within patient effect estimates.

    treangenlab/mbcausal's past year of commit activity
    Python 2 0 0 0 Updated Aug 5, 2026
  • bakeoff Public

    repository for scripts, figures, and result tables of bakeoff evaluations

    treangenlab/bakeoff's past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Jul 29, 2026
  • somatem Public

    LLM accessible long-read metagenomics pipeline with best practices

    treangenlab/somatem's past year of commit activity
    Python 4 GPL-3.0 0 10 1 Updated Jul 16, 2026
  • Strainify Public

    Strain-level abundance analysis tool for short-read metagenomics

    treangenlab/Strainify's past year of commit activity
    Python 12 MIT 0 2 0 Updated Jul 12, 2026
  • Mimic Public Forked from collaborativebioinformatics/Mimic

    Generates simulated ONT/PacBio metegenomic samples based off real microbiome sample abundances

    treangenlab/Mimic's past year of commit activity
    Python 2 MIT 1 0 1 Updated May 25, 2026
  • mft-tools Public

    Tranform DNA sequences using the Min-Frame Transformation (MFT)

    treangenlab/mft-tools's past year of commit activity
    Rust 3 MIT 0 0 0 Updated May 20, 2026
  • mft-analyses Public

    Repository of analyses for mft paper

    treangenlab/mft-analyses's past year of commit activity
    Jupyter Notebook 1 MIT 0 0 0 Updated May 20, 2026