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    15 repositories

    • scDoRI

      Public
      scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (eGRNs) from single-cell multiome data (RNA + ATAC).
      Python
      •
      MIT License
      •5•19•1•3•Updated Aug 20, 2025Aug 20, 2025

    • mofaflex

      Public
      factor models for omics data
      bioinformaticssingle-cellfactor-analysismulti-omicsmuvimofamultimodal-omics-analysis
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•15•1•0•Updated Aug 18, 2025Aug 18, 2025

    • mofax

      Public
      Work with trained factor models in Python
      scrna-seqmofaplusfactor-modelsmofa
      Jupyter Notebook
      •
      MIT License
      •14•34•3•6•Updated Oct 22, 2024Oct 22, 2024

    • mofapy2

      Public
      Multi-omics factor analysis v2
      Python
      •
      GNU Lesser General Public License v3.0
      •28•48•6•1•Updated Oct 21, 2024Oct 21, 2024

    • MOFA2

      Public
      Multi-Omics Factor Analysis
      factor-analysismulti-omicsmofa
      R
      •
      GNU Lesser General Public License v3.0
      •59•346•76•4•Updated Jun 29, 2024Jun 29, 2024

    • cellij

      Public
      Implementation of a Modular Multi-Omics Factor Model Framework
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•4•13•3•Updated Oct 19, 2023Oct 19, 2023

    • cellij-notebooks

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Sep 15, 2023Sep 15, 2023

    • MOFAdata

      Public
      Data for Multi-Omics Factor Analysis (MOFA)
      R
      •2•2•1•0•Updated Jun 9, 2023Jun 9, 2023

    • FISHFactor

      Public
      A probabilistic factor model for spatial transcriptomics data with subcellular resolution
      Jupyter Notebook
      •
      GNU Lesser General Public License v3.0
      •0•23•0•0•Updated May 3, 2023May 3, 2023

    • MOFA2_tutorials

      Public
      MOFA2 Tutorials
      HTML
      •8•6•1•1•Updated Feb 8, 2023Feb 8, 2023

    • slalom

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •10•29•6•1•Updated Feb 1, 2023Feb 1, 2023

    • MEFISTO_analyses

      Public
      Repository containing the code to reproduce the analyses contained in the MEFISTO manuscript
      R
      •2•8•0•0•Updated Jul 27, 2021Jul 27, 2021

    • MEFISTO_tutorials

      Public
      Repository containing tutorials for MEFISTO
      HTML
      •0•2•1•0•Updated Jun 28, 2021Jun 28, 2021

    • MOFA

      Public
      Multi-Omics Factor Analysis
      R
      •
      GNU Lesser General Public License v3.0
      •65•249•12•0•Updated Sep 30, 2020Sep 30, 2020

    • PEER

      Public
      PEER using MOFA
      R
      •0•1•3•0•Updated Apr 8, 2020Apr 8, 2020