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1. SCope SCope Public

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

   Python 74 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 525 195

3. AUCell AUCell Public

   AUCell: score single cells with gene regulatory networks

   R 160 28

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 69 12

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 229 45

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 43 8