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    • 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
      Other
      22813Updated Dec 23, 2024Dec 23, 2024
    • pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
      Jupyter Notebook
      Other
      1259462Updated Dec 17, 2024Dec 17, 2024
    • 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
      Other
      311921294Updated Dec 16, 2024Dec 16, 2024
    • Tools for correcting single cell barcodes for various scATAC-seq techniques.
      Shell
      32620Updated Dec 12, 2024Dec 12, 2024
    • Create regulatory regions delineation
      Python
      0100Updated Nov 15, 2024Nov 15, 2024
    • Tools for working with scATAC-seq fragment files
      Python
      0600Updated Nov 13, 2024Nov 13, 2024
    • Jupyter Notebook
      1700Updated Oct 6, 2024Oct 6, 2024
    • scforest

      Public
      scforest: a visual overview of single cell technology
      TeX
      0300Updated Aug 30, 2024Aug 30, 2024
    • biopython

      Public
      Official git repository for Biopython (converted from CVS)
      Python
      Other
      1.8k000Updated Aug 12, 2024Aug 12, 2024
    • Nova-ST

      Public
      A repository containing the analysis scripts for Nova-ST data
      Jupyter Notebook
      0800Updated Jul 1, 2024Jul 1, 2024
    • Download files from and list content of NextCloud (password protected) share directly from the command line without needing a webbrowser.
      Shell
      MIT License
      112331Updated Jun 18, 2024Jun 18, 2024
    • SpatialNF

      Public
      Spatial transcriptomics NextFlow pipelines
      Python
      GNU General Public License v3.0
      0210Updated May 16, 2024May 16, 2024
    • PUMATAC

      Public
      Pipeline for Universal Mapping of ATAC-seq
      Nextflow
      Other
      12410Updated Apr 30, 2024Apr 30, 2024
    • pycistarget is a python module to perform motif enrichment analysis in sets of regions with different tools and identify high confidence TF cistromes.
      Python
      Other
      415140Updated Apr 23, 2024Apr 23, 2024
    • DeepBrain

      Public
      DeepBrain: a collection of vertebrate sequence-based enhancer models aimed at understanding brain cell type enhancer code across and within species
      Jupyter Notebook
      Other
      0500Updated Apr 18, 2024Apr 18, 2024
    • 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.
      Python
      GNU General Public License v3.0
      1844592033Updated Apr 8, 2024Apr 8, 2024
    • SCENIC

      Public
      SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
      HTML
      GNU General Public License v3.0
      954261051Updated Apr 5, 2024Apr 5, 2024
    • arboreto

      Public
      A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.
      Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      2554281Updated Apr 5, 2024Apr 5, 2024
    • cisTopic

      Public
      cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
      HTML
      2913570Updated Apr 5, 2024Apr 5, 2024
    • ctxcore

      Public
      Core functions for pycisTarget and the SCENIC tool suite
      Python
      GNU General Public License v3.0
      6321Updated Mar 29, 2024Mar 29, 2024
    • AUCell

      Public
      AUCell: score single cells with gene regulatory networks
      R
      27135151Updated Mar 9, 2024Mar 9, 2024
    • RcisTarget: Transcription factor binding motif enrichment
      HTML
      935130Updated Mar 4, 2024Mar 4, 2024
    • shap

      Public
      A game theoretic approach to explain the output of any machine learning model.
      Jupyter Notebook
      MIT License
      3.3k000Updated Jan 22, 2024Jan 22, 2024
    • Jupyter Notebook
      21610Updated Dec 15, 2023Dec 15, 2023
    • SCENIC+ analyses
      Jupyter Notebook
      0820Updated Sep 26, 2023Sep 26, 2023
    • CSS
      0010Updated Sep 6, 2023Sep 6, 2023
    • The MendelCraft mod, introducing Mendelian genetics to the chickens of Minecraft!
      Java
      MIT License
      1530Updated Aug 2, 2023Aug 2, 2023
    • Bravo_et_al_Liver
      Jupyter Notebook
      0500Updated Jul 16, 2023Jul 16, 2023
    • LoomXpy

      Public
      Python package (compatible with SCope) to create .loom files and extend them with other data e.g.: SCENIC regulons
      Python
      MIT License
      3610Updated Jun 13, 2023Jun 13, 2023
    • R
      0010Updated May 8, 2023May 8, 2023