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@sysbiolab Bioinformatics and Systems Biology Laboratory

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    Repositories list

    14 repositories

    • RGraphSpace

      Public
      A lightweight package for representing large igraph objects in a normalized coordinate system
      R
      •
      Artistic License 2.0
      •1•5•13•0•Updated Sep 11, 2026Sep 11, 2026

    • gspacer

      Public
      0•0•0•0•Updated Sep 4, 2026Sep 4, 2026

    • GraphSpacer

      Public
      0•0•0•0•Updated Sep 3, 2026Sep 3, 2026

    • PathwaySpace

      Public
      PathwaySpace is an R package that creates landscape images from graphs containing vertices (nodes), edges (lines), and a signal associated with the vertices.
      bioinformaticsrgraph
      bioinformaticsrgraphbiological-networks
      R
      •2•3•0•0•Updated Aug 30, 2026Aug 30, 2026

    • SpotSpace

      Public
      R
      •0•0•0•0•Updated Apr 22, 2026Apr 22, 2026

    • GeneBridge

      Public
      Rooting Orthologous Genes in Large-Scale Evolutionary Analysis.
      R
      •2•7•0•0•Updated Feb 25, 2026Feb 25, 2026

    • TreeAndLeaf

      Public
      An R package for displaying binary trees, aiming to represent multiple layers of information on dendrogram leaves.
      binary-treer-packagebinary-tree-visualization
      binary-treer-packagebinary-tree-visualizationdendrogramreorganizing-dendrograms
      3•15•0•0•Updated Feb 18, 2026Feb 18, 2026

    • RedeR

      Public
      RedeRis a stand-alone Java application for interactive visualization and manipulation of nested networks.
      0•0•0•0•Updated Sep 18, 2025Sep 18, 2025

    • RTN

      Public
      Reconstruction of Transcriptional regulatory Networks and analysis of regulons
      0•0•0•0•Updated Sep 18, 2025Sep 18, 2025

    • alphafold

      Public
      Open source code for AlphaFold.
      Python
      •
      Apache License 2.0
      •2.9k•0•0•0•Updated Jun 27, 2024Jun 27, 2024

    • Sup_Material_Muzzi2022

      Public
      Supplementary material for Muzzi et al., 2022 presenting the script and data used in the study.
      R
      •0•0•0•0•Updated Oct 27, 2022Oct 27, 2022

    • Sup_Material_Mathias2021

      Public
      Supplementary material for Mathias 2021.
      0•0•0•0•Updated May 31, 2021May 31, 2021

    • SupportingMaterial_Muzzi2021

      Public
      Supplementary Material for Muzzi, 2021.
      0•0•0•0•Updated Feb 26, 2021Feb 26, 2021

    • RTN_example_TCGA_LIHC

      Public
      Example of data preprocessing for RTNsurvival, using the TCGA-LIHC cohort
      R
      •5•0•0•0•Updated Jan 28, 2019Jan 28, 2019
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