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    81 repositories

    • TF-MINDI

      Public
      Transcription Factor Motif Instance Neighborhood Decomposition and Interpretation
      Python
      •
      Other
      •2•17•3•5•Updated Apr 13, 2026Apr 13, 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-specifi…
      deep-learningsequence-modelssingle-cell-genomics
      deep-learningsequence-modelssingle-cell-genomicsscatac-seqregulatory-genomicsscverse
      Python
      •
      Other
      •9•64•7•1•Updated Apr 6, 2026Apr 6, 2026

    • ASAP

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Apr 1, 2026Apr 1, 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.
      scatac-seqhydrop
      scatac-seqhydrop
      Shell
      •4•29•3•0•Updated Apr 1, 2026Apr 1, 2026

    • pycisTopic

      Public
      pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
      Jupyter Notebook
      •
      Other
      •18•79•58•6•Updated Mar 30, 2026Mar 30, 2026

    • scatac_fragment_tools

      Public
      Tools for working with scATAC-seq fragment files
      fragmentsfragmentsingle-cell
      fragmentsfragmentsingle-cellscatac-seq
      Python
      •
      MIT License
      •1•7•0•1•Updated Feb 25, 2026Feb 25, 2026

    • ctxcore

      Public
      Core functions for pycisTarget and the SCENIC tool suite
      Python
      •
      GNU General Public License v3.0
      •9•5•2•3•Updated Jan 30, 2026Jan 30, 2026

    • 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 chromati…
      Jupyter Notebook
      •
      Other
      •53•251•193•9•Updated Jan 16, 2026Jan 16, 2026

    • GAME-DeepBICCN2-Predictor

      Public
      DeepBICCN2 Cell Type-Specific Chromatin Accessibility Predictor Container for the Genomic API for Model Evaluation (GAME)
      Python
      •0•0•0•0•Updated Jan 8, 2026Jan 8, 2026

    • GAME-BICCN-Evaluator-EnhancerLabel

      Public
      GAME container files for the BICCN evaluator (on-target enhancer cell type classification)
      Python
      •0•0•0•0•Updated Jan 8, 2026Jan 8, 2026

    • SCope

      Public
      Fast visualization tool for large-scale and high dimensional single-cell data
      awscloudreactjs
      awscloudreactjsgrpcgene-expressionsingle-cellloomlarge-scale-data-visualizationgene-regulatory-network
      Python
      •
      GNU General Public License v3.0
      •15•78•98•4•Updated Dec 16, 2025Dec 16, 2025

    • CREsted-paper

      Public
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Dec 3, 2025Dec 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 microflu…
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 10, 2025Nov 10, 2025

    • PUMATAC

      Public
      Pipeline for Universal Mapping of ATAC-seq
      pipelinenextflowsequencing
      pipelinenextflowsequencingatac-seqchromatin
      Nextflow
      •
      GNU General Public License v2.0
      •1•26•1•0•Updated Sep 23, 2025Sep 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 …
      transcription-factorstranscriptomicssingle-cell
      transcription-factorstranscriptomicssingle-cellgene-regulatory-network
      Python
      •
      GNU General Public License v3.0
      •210•595•233•5•Updated Jun 26, 2025Jun 26, 2025

    • scenicplus_core

      Public
      Collection of common algorithms and functions for all SCENIC+ related tools.
      Rust
      •0•0•0•0•Updated Jun 20, 2025Jun 20, 2025

    • create_cisTarget_databases

      Public
      Create cisTarget databases
      Python
      •7•58•38•0•Updated Jun 18, 2025Jun 18, 2025

    • mango-ingest

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Jun 12, 2025Jun 12, 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
      genomicsevolutiondeeplearning
      genomicsevolutiondeeplearningenhancersingle-cellbrain
      Jupyter Notebook
      •
      Other
      •0•8•0•0•Updated Jan 30, 2025Jan 30, 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•18•16•0•Updated Jan 21, 2025Jan 21, 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•9•0•0•Updated Oct 6, 2024Oct 6, 2024

    • scforest

      Public
      scforest: a visual overview of single cell technology
      TeX
      •1•4•0•0•Updated Aug 30, 2024Aug 30, 2024

    • biopython

      Public
      Official git repository for Biopython (converted from CVS)
      Python
      •
      Other
      •1.9k•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•28•3•0•Updated Jun 18, 2024Jun 18, 2024

    • SpatialNF

      Public
      Spatial transcriptomics NextFlow pipelines
      Python
      •
      GNU General Public License v3.0
      •2•6•1•0•Updated May 16, 2024May 16, 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•481•112•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-learningscalable
      pythonmachine-learningscalablerandom-forestnetworkinferencegene-regulationensemble-learningdaskgradient-boosting
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •35•66•28•2•Updated Apr 5, 2024Apr 5, 2024

    • cisTopic

      Public
      cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
      HTML
      •27•145•7•0•Updated Apr 5, 2024Apr 5, 2024
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