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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 262 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 baskerville Public

    Machine learning methods for DNA sequence analysis.

    Python 66 18

Repositories

Showing 10 of 67 repositories
  • ap1-lung-paper Public

    Companion R code for "AP-1 regulates lung developmental versus fibrotic extracellular matrix transcriptional programs"

    calico/ap1-lung-paper's past year of commit activity
    R 0 MIT 0 0 0 Updated Sep 10, 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 0 1 0 Updated Sep 10, 2026
  • glycoviz Public

    Glycan analysis application with build-in validation algorithm.

    calico/glycoviz's past year of commit activity
    Python 0 MIT 0 0 3 Updated Sep 10, 2026
  • mzkitcpp Public

    R package of mass spectrometry utility functions and processing algorithms written in C++

    C++ 1 MIT 0 0 0 Updated Sep 10, 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 Sep 6, 2026
  • shorkie-paper Public

    Data processing and analyses related to regulatory sequence prediction in yeast.

    calico/shorkie-paper's past year of commit activity
    Jupyter Notebook 14 Apache-2.0 3 2 1 Updated Sep 2, 2026
  • majec Public

    Initial release of MAJEC: a tool for unified gene, isoform, and locus-level transposable element quantification from RNA-seq

    calico/majec's past year of commit activity
    Python 5 Apache-2.0 0 0 0 Updated Aug 31, 2026
  • tools-patched Public

    Patches and updates for `concurrency_tools.py` and `napari_in_subprocess.py`

    calico/tools-patched's past year of commit activity
    Python 0 GPL-2.0 1 0 0 Updated Aug 4, 2026
  • sniff Public

    Borzoi-informed fine mapping with PolyFun

    calico/sniff's past year of commit activity
    Python 0 MIT 0 0 0 Updated Jul 23, 2026
  • baskerville Public

    Machine learning methods for DNA sequence analysis.

    calico/baskerville's past year of commit activity
    Python 66 Apache-2.0 18 2 3 Updated Jul 20, 2026

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