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    13 repositories

    • InferelatorJL

      Public
      Julia
      •3•1•0•0•Updated Apr 15, 2026Apr 15, 2026

    • RapidRecall

      Public
      Codebase for figure generation for the human CD4+ rapid recall manuscript
      R
      •1•0•0•0•Updated Mar 24, 2026Mar 24, 2026

    • maxATAC

      Public
      Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
      chip-seqdeeplearningatac-seq
      chip-seqdeeplearningatac-seqtranscription-factor-bindinggenome-analysismaxatac
      Python
      •
      Apache License 2.0
      •11•29•3•5•Updated Mar 19, 2026Mar 19, 2026

    • quant-maxATAC

      Public
      quantitative maxATAC
      Python
      •
      Apache License 2.0
      •2•0•1•3•Updated Dec 10, 2025Dec 10, 2025

    • quant-maxATAC_data

      Public
      quantitative models
      0•0•0•0•Updated Oct 2, 2025Oct 2, 2025

    • snakeCHIP

      Public
      A snakemake workflow for ChIP-seq data processing
      Python
      •
      MIT License
      •1•1•0•0•Updated Aug 31, 2025Aug 31, 2025

    • Interactive_visualization

      Public
      HAE scripts codebank
      R
      •0•0•0•0•Updated Apr 7, 2023Apr 7, 2023

    • maxATAC_data

      Public
      This repo contains additional resources for the maxATAC Python package.
      chip-seqdeeplearningatac-seq
      chip-seqdeeplearningatac-seqmaxatac
      Shell
      •1•4•1•0•Updated Nov 29, 2022Nov 29, 2022

    • snakeATAC

      Public
      A snakemake workflow to process ATAC-seq data
      R
      •
      Apache License 2.0
      •4•0•0•0•Updated Nov 29, 2022Nov 29, 2022

    • infTRN_lassoStARS

      Public
      Transcriptional regulatory network inference from gene expression and prior information with LASSO-StARS
      Fortran
      •6•0•0•0•Updated May 3, 2022May 3, 2022

    • CHEERS

      Public
      Python
      •4•0•0•0•Updated Oct 17, 2021Oct 17, 2021

    • Th17_TRN_Networks

      Public
      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
      •1•0•0•0•Updated Feb 20, 2019Feb 20, 2019

    • ILCnetworks

      Public
      Gene regulatory networks for intestinal innate lymphoid cells
      Jupyter Notebook
      •2•0•0•0•Updated Feb 19, 2019Feb 19, 2019
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