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@aertslab

aertslab

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  1. SCope SCope Public

    Fast visualization tool for large-scale and high dimensional single-cell data

    Python 77 15

  2. pySCENIC pySCENIC Public

    pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene reg…

    Python 567 198

  3. AUCell AUCell Public

    AUCell: score single cells with gene regulatory networks

    R 180 30

  4. pycisTopic pycisTopic Public

    pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.

    Jupyter Notebook 78 14

  5. scenicplus scenicplus Public

    SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.

    Jupyter Notebook 242 51

  6. CREsted CREsted Public

    CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.

    Python 55 9

Repositories

Showing 10 of 78 repositories
  • TF-MINDI Public

    Transcription Factor Motif Instance Neighborhood Decomposition and Interpretation

    aertslab/TF-MINDI’s past year of commit activity
    Python 10 1 0 4 Updated Jan 6, 2026
  • CREsted Public

    CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.

    aertslab/CREsted’s past year of commit activity
    Python 55 9 7 (1 issue needs help) 5 Updated Jan 6, 2026
  • single_cell_toolkit Public

    Tools for correcting single cell barcodes for various scATAC-seq techniques and creating fragment files and spltting BAM files per cluster.

    aertslab/single_cell_toolkit’s past year of commit activity
    Shell 29 4 3 0 Updated Dec 19, 2025
  • pycisTopic Public

    pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.

    aertslab/pycisTopic’s past year of commit activity
    Jupyter Notebook 78 14 57 5 Updated Dec 19, 2025
  • scatac_fragment_tools Public

    Tools for working with scATAC-seq fragment files

    aertslab/scatac_fragment_tools’s past year of commit activity
    Python 7 MIT 0 0 1 Updated Dec 16, 2025
  • SCope Public

    Fast visualization tool for large-scale and high dimensional single-cell data

    aertslab/SCope’s past year of commit activity
    Python 77 GPL-3.0 15 98 (2 issues need help) 4 Updated Dec 16, 2025
  • CREsted-paper Public
    aertslab/CREsted-paper’s past year of commit activity
    Jupyter Notebook 2 MIT 0 0 0 Updated Dec 3, 2025
  • HyDrop_v2_paper Public

    To facilitate the cost-effective generation of large scATAC-seq atlases for deep learning model training, we developed a new version of the open-source microfluidic system HyDrop with increased sensitivity and scale: HyDrop v2.

    aertslab/HyDrop_v2_paper’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Nov 10, 2025
  • PUMATAC Public

    Pipeline for Universal Mapping of ATAC-seq

    aertslab/PUMATAC’s past year of commit activity
    Nextflow 25 GPL-2.0 1 1 0 Updated Sep 23, 2025
  • pySCENIC Public

    pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

    aertslab/pySCENIC’s past year of commit activity
    Python 567 GPL-3.0 198 230 4 Updated Jun 26, 2025
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