Repositories list

• RGraphSpace

  Public
  A lightweight package for representing large igraph objects in a normalized coordinate system

  R

  •0•2•0•0•Updated Jan 19, 2026Jan 19, 2026

• SpotSpace

  Public
  R

  •0•0•0•0•Updated Jan 19, 2026Jan 19, 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+ 1biological-networks

  R

  •2•3•0•0•Updated Nov 5, 2025Nov 5, 2025

• 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

• TreeAndLeaf

  Public
  An R package for displaying binary trees, aiming to represent multiple layers of information on dendrogram leaves.

  binary-treer-packagebinary-tree-visualization+ 2dendrogramreorganizing-dendrograms

  R

  •3•15•2•0•Updated Sep 18, 2025Sep 18, 2025

• hexcore-project

  Public archive
  Jupyter Notebook

  •0•0•0•0•Updated Jul 9, 2025Jul 9, 2025

• neuriteScan

  Public
  An R Package for neurite image analysis.

  HTML

  •1•1•0•0•Updated Feb 6, 2025Feb 6, 2025

• alphafold

  Public
  Open source code for AlphaFold.

  Python

  •

  Apache License 2.0

  •2.5k•0•0•0•Updated Jun 27, 2024Jun 27, 2024

• GeneBridge

  Public
  Rooting Orthologous Genes in Large-Scale Evolutionary Analysis.

  R

  •2•7•1•0•Updated Jan 21, 2024Jan 21, 2024

• 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