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    10 repositories

    • ALPINE

      Public
      ALPINE is a semi-supervised non-negative matrix factorization (NMF) framework designed to effectively distinguish between multiple phenotypic conditions based on shared biological factors, while also providing direct interpretability of condition-associated genes.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 11, 2024Nov 11, 2024

    • seismic

      Public
      Seismic R package. Discover cell type-trait associations in minutes for GWAS and single-cell RNA-sequencing data
      gwassingle-cellscrna
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •4•9•1•0•Updated Sep 30, 2024Sep 30, 2024

    • ANDES

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Aug 28, 2024Aug 28, 2024

    • flambe

      Public
      datasets for tissue and tool named entity recognition, annotation files for biological workflow extraction, and disambiguation files
      natural-language-processingbioinformaticsnamed-entity-recognitionsingle-cellbionlpmultiverse-analysis
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •0•4•0•0•Updated Jul 8, 2024Jul 8, 2024

    • biomedical

      Public
      Tools for curating biomedical training data for large-scale language modeling
      Python
      •116•1•0•0•Updated Jun 4, 2024Jun 4, 2024

    • ar-biorxiv-style

      Public
      A Latex style and template for paper preprints (based on NIPS style)
      TeX
      •
      MIT License
      •314•0•0•0•Updated Mar 12, 2024Mar 12, 2024

    • splitpea

      Public
      A tool for calculating PPI network rewiring due to alternative splicing
      bioinformaticscancerprotein-protein-interactionppi-networkssplicing
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Jan 15, 2024Jan 15, 2024

    • ETNA

      Public
      Embeddings to Network Alignment - align biological networks between two species
      computational-biologynetwork-alignmentbioinformatics-toolppi-networksprotein-protein-interaction-network
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•9•0•1•Updated Sep 8, 2023Sep 8, 2023

    • kraken2

      Public
      The second version of the Kraken taxonomic sequence classification system
      C++
      •
      MIT License
      •273•0•0•0•Updated Jun 1, 2021Jun 1, 2021

    • krakenuniq

      Public
      🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
      C++
      •43•0•0•0•Updated May 27, 2021May 27, 2021