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    21 repositories

    • SimiCviz

      Public
      Official repository for SimiCviz tools, an R package for gene regulatory network visualization tools.
      HTML
      •
      Other
      •1•0•0•0•Updated Apr 21, 2026Apr 21, 2026

    • SimiCPipeline

      Public
      Official repository for SimiCPipeline tools, a single-cell gene regulatory network inference framework.
      Jupyter Notebook
      •
      MIT License
      •0•2•0•1•Updated Mar 31, 2026Mar 31, 2026

    • SNMF-paper

      Public
      Reference-free deconvolution benchmarking, including novel spatial NMF method.
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Mar 21, 2026Mar 21, 2026

    • SNMF

      Public
      Spatial Non-Negative Matrix Factorization
      R
      •
      MIT License
      •0•1•0•0•Updated Mar 17, 2026Mar 17, 2026

    • Functional-cart-atlas

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Mar 17, 2026Mar 17, 2026

    • DeepRBP

      Public
      Python
      •3•3•1•0•Updated Jan 21, 2026Jan 21, 2026

    • Sweetwater

      Public
      Official repository of the data-driven deconvolution approach Sweetwater.
      Python
      •
      MIT License
      •0•15•0•0•Updated Sep 9, 2025Sep 9, 2025

    • SENA

      Public
      Official repository for the SENA-discrepancy-VAE model.
      bioinformaticscrlinterpretability
      bioinformaticscrlinterpretability
      Python
      •
      MIT License
      •1•9•1•0•Updated Aug 20, 2025Aug 20, 2025

    • RYGB

      Public
      Python
      •1•0•0•0•Updated Jul 16, 2025Jul 16, 2025

    • JIND-Multi

      Public
      An extended framework to leverage multiple labeled datasets for the automatic annotation of single-cell RNA and ATAC data
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jul 10, 2025Jul 10, 2025

    • GraphEmb

      Public
      Python
      •
      MIT License
      •3•12•0•0•Updated May 21, 2025May 21, 2025

    • ELATUS

      Public
      R
      •1•14•0•0•Updated Apr 2, 2025Apr 2, 2025

    • manuscript_scRNAseq_lncRNAs

      Public
      Repository containing all the scripts necessary for generating the results in the manuscript
      R
      •2•7•0•0•Updated Nov 18, 2024Nov 18, 2024

    • GUEST

      Public
      This is a package for evaluating prediction models based on Graph Embedding methodologies.
      Jupyter Notebook
      •
      MIT License
      •0•10•0•0•Updated Nov 11, 2024Nov 11, 2024

    • transfer_example

      Public
      LEts gooo
      0•2•0•0•Updated Aug 9, 2024Aug 9, 2024

    • MDS_5q_2023

      Public
      Code of paper: Single-cell transcriptional profile of CD34+ hematopoietic progenitor cells from del(5q) myelodysplastic syndromes and impact of lenalidomide
      R
      •
      MIT License
      •4•4•0•0•Updated Apr 17, 2024Apr 17, 2024

    • NetActivityTrain

      Public
      Nextflow pipeline to train models for NetActivity
      Groovy
      •
      MIT License
      •1•0•0•0•Updated Apr 9, 2024Apr 9, 2024

    • GeNNius

      Public
      GeNNius: An ultrafast drug-target interaction inference method based on graph neural networks
      Python
      •
      MIT License
      •4•15•1•0•Updated Mar 8, 2024Mar 8, 2024

    • TraRe

      Public
      This repository contains the TraRe package, from the paper "Bayesian Machine Learning Enables Identification of Transcriptional Network Disruptions Associated w…
      R
      •
      Other
      •0•5•0•0•Updated Mar 6, 2024Mar 6, 2024

    • JIND

      Public
      Jupyter Notebook
      •
      MIT License
      •3•0•0•0•Updated Aug 14, 2023Aug 14, 2023

    • TraRe-materials

      Public
      Material for the reproducibility of figures and tables from TraRe project.
      HTML
      •0•1•0•0•Updated Dec 7, 2022Dec 7, 2022
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