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    • Julia
      3100Updated Apr 15, 2026Apr 15, 2026
    • Codebase for figure generation for the human CD4+ rapid recall manuscript
      R
      1000Updated Mar 24, 2026Mar 24, 2026
    • maxATAC

      Public
      Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
      Python
      Apache License 2.0
      112935Updated Mar 19, 2026Mar 19, 2026
    • quantitative maxATAC
      Python
      Apache License 2.0
      2013Updated Dec 10, 2025Dec 10, 2025
    • quantitative models
      0000Updated Oct 2, 2025Oct 2, 2025
    • snakeCHIP

      Public
      A snakemake workflow for ChIP-seq data processing
      Python
      MIT License
      1100Updated Aug 31, 2025Aug 31, 2025
    • HAE scripts codebank
      R
      0000Updated Apr 7, 2023Apr 7, 2023
    • This repo contains additional resources for the maxATAC Python package.
      Shell
      1410Updated Nov 29, 2022Nov 29, 2022
    • snakeATAC

      Public
      A snakemake workflow to process ATAC-seq data
      R
      Apache License 2.0
      4000Updated Nov 29, 2022Nov 29, 2022
    • Transcriptional regulatory network inference from gene expression and prior information with LASSO-StARS
      Fortran
      6000Updated May 3, 2022May 3, 2022
    • CHEERS

      Public
      Python
      4000Updated Oct 17, 2021Oct 17, 2021
    • Data and notebooks for "Leveraging ATAC-seq data for transcriptional regulatory inference in Th17 Cells" by Miraldi et al.
      Jupyter Notebook
      Apache License 2.0
      1000Updated Feb 20, 2019Feb 20, 2019
    • Gene regulatory networks for intestinal innate lymphoid cells
      Jupyter Notebook
      2000Updated Feb 19, 2019Feb 19, 2019
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