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    73 repositories

    • shorkie-paper

      Public
      Data processing and analyses related to regulatory sequence prediction in yeast.
      Jupyter Notebook
      •
      Apache License 2.0
      •3•14•2•0•Updated Oct 14, 2026Oct 14, 2026

    • drido-multiomic-paper

      Public
      Companion R code for "A multiomic lifespan signature in genetically diverse, diet-restricted mice"
      R
      •
      MIT License
      •1•0•1•0•Updated Oct 13, 2026Oct 13, 2026

    • baskerville

      Public
      PyTorch models of DNA sequence to regulatory activity
      deep-learninggenomicspytorch
      deep-learninggenomicspytorchgene-regulation
      Python
      •
      Apache License 2.0
      •0•8•0•2•Updated Oct 10, 2026Oct 10, 2026

    • glycoviz

      Public
      Glycan analysis application with build-in validation algorithm.
      Python
      •
      MIT License
      •0•2•0•3•Updated Oct 10, 2026Oct 10, 2026

    • mzkitcpp

      Public
      R package of mass spectrometry utility functions and processing algorithms written in C++
      C++
      •
      MIT License
      •0•1•0•0•Updated Oct 9, 2026Oct 9, 2026

    • GIMAP6_CVD_Analysis-

      Public
      Code and analysis for the association of GIMAP6 variants with cardiovascular disease in the All of Us cohort, as described in Chen X et al., 2025.
      Python
      •
      MIT License
      •1•0•0•0•Updated Oct 8, 2026Oct 8, 2026

    • westminster

      Public
      Benchmarking baskerville models for regulatory sequence activity prediction
      Python
      •
      Apache License 2.0
      •3•2•1•2•Updated Oct 5, 2026Oct 5, 2026

    • multi-ism

      Public
      Python
      •
      Apache License 2.0
      •0•2•0•0•Updated Oct 5, 2026Oct 5, 2026

    • borzoi-paper

      Public
      Analyses related to the Borzoi paper.
      Jupyter Notebook
      •
      Apache License 2.0
      •4•32•2•0•Updated Oct 1, 2026Oct 1, 2026

    • borzoi

      Public
      RNA-seq prediction with deep convolutional neural networks.
      Python
      •
      Apache License 2.0
      •33•267•2•0•Updated Sep 30, 2026Sep 30, 2026

    • baskerville-tf

      Public
      Machine learning methods for DNA sequence analysis.
      Python
      •
      Apache License 2.0
      •18•66•2•1•Updated Sep 30, 2026Sep 30, 2026

    • metisotopes

      Public
      Pipeline and utilities for stable isotope-labeled (SIL) metabolomics data
      R
      •
      MIT License
      •0•0•0•0•Updated Sep 23, 2026Sep 23, 2026

    • claman

      Public
      Calico Lipidomics and Metabolomics (CLaM) Analysis provides a suite of functions which support data manipulation, statistical analysis and visualizations of mzr…
      R
      •
      Other
      •0•3•5•1•Updated Sep 18, 2026Sep 18, 2026

    • baskerville-yeast

      Public
      Machine learning methods for DNA sequence analysis (Yeast / LLM fork).
      Python
      •
      Apache License 2.0
      •0•2•0•1•Updated Sep 18, 2026Sep 18, 2026

    • hdwig

      Public
      Genomic coverage tracks in HDF5
      Python
      •
      MIT License
      •0•1•0•0•Updated Sep 15, 2026Sep 15, 2026

    • ap1-lung-paper

      Public
      Companion R code for "AP-1 regulates lung developmental versus fibrotic extracellular matrix transcriptional programs"
      R
      •
      MIT License
      •0•0•0•0•Updated Sep 10, 2026Sep 10, 2026

    • qtl-bench

      Public
      Fine-mapped GTEx QTL benchmark sets for evaluating sequence-to-function variant effect prediction
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Sep 7, 2026Sep 7, 2026

    • majec

      Public
      Initial release of MAJEC: a tool for unified gene, isoform, and locus-level transposable element quantification from RNA-seq
      Python
      •
      Apache License 2.0
      •0•8•0•0•Updated Aug 31, 2026Aug 31, 2026

    • tools-patched

      Public
      Patches and updates for `concurrency_tools.py` and `napari_in_subprocess.py`
      Python
      •
      GNU General Public License v2.0
      •1•0•0•0•Updated Aug 4, 2026Aug 4, 2026

    • sniff

      Public
      Borzoi-informed fine mapping with PolyFun
      Python
      •
      MIT License
      •0•1•0•0•Updated Jul 23, 2026Jul 23, 2026

    • calicolabs-auto-anubis-vialweighing

      Public
      ANUBIS: An automated vial weighing system with the Meca500 robotic arm
      Python
      •
      MIT License
      •0•0•0•1•Updated Jun 11, 2026Jun 11, 2026

    • scnym

      Public
      Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
      rna-seqsingle-cellsingle-cell-genomics
      rna-seqsingle-cellsingle-cell-genomicssemi-supervisedadversarial-training
      Python
      •
      Apache License 2.0
      •13•78•3•1•Updated Jun 10, 2026Jun 10, 2026

    • metstats

      Public
      Library for standardized analysis and visualization of metabolomics data
      R
      •
      MIT License
      •1•3•0•1•Updated Jun 10, 2026Jun 10, 2026

    • CalicoLipidLibrary

      Public
      In silico Lipid fragmentation patterns
      Python
      •
      MIT License
      •1•0•4•1•Updated May 27, 2026May 27, 2026

    • triplet_tumbling_microscopy

      Public
      Software to operate the triplet tumbling microscope and analyze resulting data
      Python
      •
      MIT License
      •0•0•0•0•Updated May 5, 2026May 5, 2026

    • ukbb-mri-sseg

      Public
      UKBB MRI semantic segmentation for Abdominal Dixon and other modalities
      5•13•0•0•Updated Apr 8, 2026Apr 8, 2026

    • Remote-Camera-Monitoring

      Public
      0•1•0•0•Updated Mar 30, 2026Mar 30, 2026

    • msTrawler

      Public
      R
      •
      GNU General Public License v2.0
      •2•9•0•0•Updated Mar 22, 2026Mar 22, 2026

    • mouse_cardiac_mri_segmentation

      Public
      Code for publication "Automated cardiac MRI analysis for robust profiling of heart failure models in mice"
      Python
      •
      MIT License
      •0•1•0•3•Updated Feb 11, 2026Feb 11, 2026

    • calico-automation-plate-chillers

      Public
      MIT License
      •0•0•0•0•Updated Jan 27, 2026Jan 27, 2026
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