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    75 repositories

    • pycisTopic

      Public
      pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
      Jupyter Notebook
      •
      Other
      •12•68•50•4•Updated Jun 18, 2025Jun 18, 2025

    • create_cisTarget_databases

      Public
      Create cisTarget databases
      Python
      •7•52•35•0•Updated Jun 18, 2025Jun 18, 2025

    • 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.
      deep-learningsequence-modelssingle-cell-genomicsscatac-seqregulatory-genomicsscverse
      Python
      •
      Other
      •7•39•4•4•Updated Jun 17, 2025Jun 17, 2025

    • mango-ingest

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Jun 12, 2025Jun 12, 2025

    • scatac_fragment_tools

      Public
      Tools for working with scATAC-seq fragment files
      fragmentsfragmentsingle-cellscatac-seq
      Python
      •0•6•0•1•Updated Jun 11, 2025Jun 11, 2025

    • CREsted-paper

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Apr 23, 2025Apr 23, 2025

    • Nova-ST

      Public
      A repository containing the analysis scripts for Nova-ST data
      Jupyter Notebook
      •0•9•1•0•Updated Apr 3, 2025Apr 3, 2025

    • DeepBrain

      Public
      DeepBrain: a collection of vertebrate sequence-based enhancer models aimed at understanding brain cell type enhancer code across and within species
      genomicsevolutiondeeplearningenhancersingle-cellbrain
      Jupyter Notebook
      •
      Other
      •0•6•0•0•Updated Jan 30, 2025Jan 30, 2025

    • 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
      •
      Other
      •42•227•158•7•Updated Jan 23, 2025Jan 23, 2025

    • pycistarget

      Public
      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
      •4•17•16•0•Updated Jan 21, 2025Jan 21, 2025

    • 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.
      scatac-seqhydrop
      Shell
      •4•27•3•0•Updated Jan 6, 2025Jan 6, 2025

    • regulatory_regions_delineation

      Public
      Create regulatory regions delineation
      Python
      •0•1•0•0•Updated Nov 15, 2024Nov 15, 2024

    • PUMATAC_tutorial

      Public
      Jupyter Notebook
      •2•8•0•0•Updated Oct 6, 2024Oct 6, 2024

    • scforest

      Public
      scforest: a visual overview of single cell technology
      TeX
      •1•3•0•0•Updated Aug 30, 2024Aug 30, 2024

    • biopython

      Public
      Official git repository for Biopython (converted from CVS)
      Python
      •
      Other
      •1.8k•0•0•0•Updated Aug 12, 2024Aug 12, 2024

    • nextcloud_share_url_downloader

      Public
      Download files from and list content of NextCloud (password protected) share directly from the command line without needing a webbrowser.
      Shell
      •
      MIT License
      •11•26•3•0•Updated Jun 18, 2024Jun 18, 2024

    • SpatialNF

      Public
      Spatial transcriptomics NextFlow pipelines
      Python
      •
      GNU General Public License v3.0
      •1•4•1•0•Updated May 16, 2024May 16, 2024

    • PUMATAC

      Public
      Pipeline for Universal Mapping of ATAC-seq
      pipelinenextflowsequencingatac-seqchromatin
      Nextflow
      •
      Other
      •1•25•1•0•Updated Apr 30, 2024Apr 30, 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.
      transcription-factorstranscriptomicssingle-cellgene-regulatory-network
      Python
      •
      GNU General Public License v3.0
      •193•514•221•3•Updated 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
      •98•456•111•1•Updated Apr 5, 2024Apr 5, 2024

    • arboreto

      Public
      A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.
      pythonmachine-learningscalablerandom-forestnetworkinferencegene-regulationensemble-learningdaskgradient-boosting
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •31•59•28•1•Updated Apr 5, 2024Apr 5, 2024

    • cisTopic

      Public
      cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
      HTML
      •28•140•7•0•Updated Apr 5, 2024Apr 5, 2024

    • ctxcore

      Public
      Core functions for pycisTarget and the SCENIC tool suite
      Python
      •
      GNU General Public License v3.0
      •7•5•2•1•Updated Mar 29, 2024Mar 29, 2024

    • AUCell

      Public
      AUCell: score single cells with gene regulatory networks
      R
      •28•154•16•1•Updated Mar 9, 2024Mar 9, 2024

    • RcisTarget

      Public
      RcisTarget: Transcription factor binding motif enrichment
      r-package
      HTML
      •9•41•14•0•Updated Mar 4, 2024Mar 4, 2024

    • shap

      Public
      A game theoretic approach to explain the output of any machine learning model.
      Jupyter Notebook
      •
      MIT License
      •3.4k•0•0•0•Updated Jan 22, 2024Jan 22, 2024

    • scATAC-seq_benchmark

      Public
      Jupyter Notebook
      •3•17•1•0•Updated Dec 15, 2023Dec 15, 2023

    • scenicplus_analyses

      Public
      SCENIC+ analyses
      Jupyter Notebook
      •1•14•2•0•Updated Sep 26, 2023Sep 26, 2023

    • spatial_fly_website

      Public
      CSS
      •0•0•2•0•Updated Sep 6, 2023Sep 6, 2023

    • MendelCraft

      Public
      The MendelCraft mod, introducing Mendelian genetics to the chickens of Minecraft!
      Java
      •
      MIT License
      •1•5•3•0•Updated Aug 2, 2023Aug 2, 2023