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Calico

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  1. basenji basenji Public

    Sequential regulatory activity predictions with deep convolutional neural networks.

    Python 475 137

  2. borzoi borzoi Public

    RNA-seq prediction with deep convolutional neural networks.

    Python 267 33

  3. scBasset scBasset Public

    Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.

    Jupyter Notebook 102 13

  4. solo solo Public archive

    software to detect doublets

    Python 98 14

  5. scnym scnym Public

    Semi-supervised adversarial neural networks for classification of single cell transcriptomics data

    Python 78 13

  6. baskerville-tf baskerville-tf Public

    Machine learning methods for DNA sequence analysis.

    Python 66 18

Repositories

Showing 10 of 73 repositories
  • GIMAP6_CVD_Analysis- Public Forked from xiangchennih-25/GIMAP6_CVD_Analysis-

    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.

    calico/GIMAP6_CVD_Analysis-'s past year of commit activity
    Python 0 MIT 1 0 1 Updated Oct 6, 2026
  • drido-multiomic-paper Public

    Companion R code for "A multiomic lifespan signature in genetically diverse, diet-restricted mice"

    calico/drido-multiomic-paper's past year of commit activity
    R 0 MIT 1 1 0 Updated Oct 6, 2026
  • baskerville Public

    PyTorch models of DNA sequence to regulatory activity

    calico/baskerville's past year of commit activity
    Python 0 Apache-2.0 0 0 1 Updated Oct 5, 2026
  • westminster Public

    Benchmarking baskerville models for regulatory sequence activity prediction

    calico/westminster's past year of commit activity
    Python 2 Apache-2.0 3 1 2 Updated Oct 5, 2026
  • multi-ism Public
    calico/multi-ism's past year of commit activity
    Python 1 Apache-2.0 0 0 0 Updated Oct 5, 2026
  • glycoviz Public

    Glycan analysis application with build-in validation algorithm.

    calico/glycoviz's past year of commit activity
    Python 2 MIT 0 0 1 Updated Oct 2, 2026
  • borzoi-paper Public

    Analyses related to the Borzoi paper.

    calico/borzoi-paper's past year of commit activity
    Jupyter Notebook 32 Apache-2.0 4 2 0 Updated Oct 1, 2026
  • borzoi Public

    RNA-seq prediction with deep convolutional neural networks.

    calico/borzoi's past year of commit activity
    Python 267 Apache-2.0 33 2 0 Updated Sep 30, 2026
  • baskerville-tf Public

    Machine learning methods for DNA sequence analysis.

    calico/baskerville-tf's past year of commit activity
    Python 66 Apache-2.0 18 2 1 Updated Oct 1, 2026
  • metisotopes Public

    Pipeline and utilities for stable isotope-labeled (SIL) metabolomics data

    calico/metisotopes's past year of commit activity
    R 0 MIT 0 0 0 Updated Sep 23, 2026

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