Repositories list

• Inferelator_Julia

  Public
  Julia

  •2•1•0•0•Updated May 30, 2025May 30, 2025

• RapidRecall

  Public
  Codebase for figure generation for the human CD4+ rapid recall manuscript

  R

  •0•0•0•0•Updated Apr 17, 2025Apr 17, 2025

• maxATAC

  Public
  Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks

  chip-seqdeeplearningatac-seq+ 3transcription-factor-bindinggenome-analysismaxatac

  Python

  •

  Apache License 2.0

  •11•28•3•3•Updated Apr 11, 2025Apr 11, 2025

• snakeCHIP

  Public
  A snakemake workflow for ChIP-seq data processing

  Python

  •

  MIT License

  •1•0•0•0•Updated Mar 18, 2025Mar 18, 2025

• JuliaInferelator_V2

  Public
  Version 2 of the JuliaInferelator

  Julia

  •0•0•0•0•Updated Oct 11, 2024Oct 11, 2024

• 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+ 1maxatac

  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