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    57 repositories

    • 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•0•0•3•Updated Feb 11, 2026Feb 11, 2026

    • baskerville

      Public
      Machine learning methods for DNA sequence analysis.
      Python
      •
      Apache License 2.0
      •17•57•1•3•Updated Feb 2, 2026Feb 2, 2026

    • scnym

      Public
      Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
      rna-seqsingle-cellsingle-cell-genomicssemi-supervisedadversarial-training
      Python
      •
      Apache License 2.0
      •13•77•7•6•Updated Jan 23, 2026Jan 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•6•0•Updated Jan 15, 2026Jan 15, 2026

    • basenji

      Public
      Sequential regulatory activity predictions with deep convolutional neural networks.
      Python
      •
      Apache License 2.0
      •136•464•83•5•Updated Jan 15, 2026Jan 15, 2026

    • sae-borzoi

      Public
      Sparse autoencoder interpretability for the Borzoi model
      Python
      •
      MIT License
      •0•3•0•0•Updated Dec 22, 2025Dec 22, 2025

    • borzoi-paper

      Public
      Analyses related to the Borzoi paper.
      Jupyter Notebook
      •
      Apache License 2.0
      •4•25•2•0•Updated Dec 14, 2025Dec 14, 2025

    • westminster

      Public
      Benchmarking baskerville models for regulatory sequence activity prediction
      Python
      •
      Apache License 2.0
      •3•2•1•2•Updated Oct 24, 2025Oct 24, 2025

    • vworks-atc-plugin

      Public
      VWorks plugin for Thermofisher ATC
      C#
      •
      MIT License
      •1•1•0•1•Updated Oct 23, 2025Oct 23, 2025

    • calicolabs-auto-anubis-vialweighing

      Public
      ANUBIS: An automated vial weighing system with the Meca500 robotic arm
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 29, 2025Sep 29, 2025

    • shorkie-paper

      Public
      Data processing and analyses related to regulatory sequence prediction in yeast.
      Python
      •
      Apache License 2.0
      •3•6•1•0•Updated Sep 12, 2025Sep 12, 2025

    • scBasset

      Public
      Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
      Jupyter Notebook
      •
      Apache License 2.0
      •13•100•3•0•Updated Sep 9, 2025Sep 9, 2025

    • vworks-phenix-plugin

      Public
      VWorks Driver for Perkin Elmer Phenix
      C#
      •
      MIT License
      •0•3•0•0•Updated Sep 8, 2025Sep 8, 2025

    • vworks-mantis-plugin

      Public
      Driver for controlling Formulatrix Mantis through VWorks
      C#
      •
      MIT License
      •0•3•0•0•Updated Sep 8, 2025Sep 8, 2025

    • baskerville-yeast

      Public
      Machine learning methods for DNA sequence analysis (Yeast / LLM fork).
      Python
      •
      Apache License 2.0
      •0•1•0•1•Updated Sep 8, 2025Sep 8, 2025

    • Heterochronic_myeloidCellTransplantation

      Public
      This GitHub repository documents the core analyses of scRNA-seq and Spatial-seq data of microglia and heterochronic myeloid cell transplantation experiments.
      R
      •
      MIT License
      •0•0•0•0•Updated Sep 7, 2025Sep 7, 2025

    • borzoi

      Public
      RNA-seq prediction with deep convolutional neural networks.
      Python
      •
      Apache License 2.0
      •30•226•8•3•Updated Aug 28, 2025Aug 28, 2025

    • msTrawler

      Public
      R
      •
      GNU General Public License v2.0
      •2•9•0•0•Updated Jul 23, 2025Jul 23, 2025

    • HE-regression

      Public
      R
      •
      MIT License
      •1•0•0•0•Updated Jul 9, 2025Jul 9, 2025

    • catnap

      Public
      CATNAP-related code
      Python
      •
      MIT License
      •1•2•1•9•Updated May 13, 2025May 13, 2025

    • bidac_induced_protein_degradation_analysis

      Public
      This repository contains accompanying analysis code for the paper "Morphological and genetic screens reveal mechanisms of BiDAC-induced plasma membrane protein …
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 29, 2025Mar 29, 2025

    • opencpr

      Public
      Landing zone for the Open source Calico Pathway Resources (CPR) project.
      Python
      •
      MIT License
      •1•0•0•0•Updated Mar 27, 2025Mar 27, 2025

    • metstats

      Public
      Library for standardized analysis and visualization of metabolomics data
      R
      •
      MIT License
      •1•3•0•0•Updated Mar 18, 2025Mar 18, 2025

    • CalicoLipidLibrary

      Public
      In silico Lipid fragmentation patterns
      Python
      •
      MIT License
      •1•0•3•1•Updated Mar 13, 2025Mar 13, 2025

    • do_bwd

      Public
      Python implementation of extracting body weight dynamics in diversity outbred mice using ARHMM.
      time-seriesgeneticsvariational-inferencebody-weightcox-proportional-hazardarhmm
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Feb 25, 2025Feb 25, 2025

    • solo

      Public
      software to detect doublets
      Python
      •
      MIT License
      •14•96•7•1•Updated Dec 28, 2024Dec 28, 2024

    • romic

      Public archive
      romic represents high-dimensional measurements by persistently tracking features, samples, and measurements as a dataset is modified and reformatted. It provide…
      R
      •
      Other
      •1•5•7•0•Updated Sep 25, 2024Sep 25, 2024

    • calicolabs-piccolo

      Public
      Python
      •
      Apache License 2.0
      •1•2•0•0•Updated Sep 16, 2024Sep 16, 2024

    • DRiDO_Paper_Release

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 19, 2024Aug 19, 2024

    • impulse

      Public
      Fit phenomenological sigmoid and impulse curves with priors to improve interpretability
      R
      •
      MIT License
      •2•10•1•0•Updated May 29, 2024May 29, 2024