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    28 repositories

    • multideconv

      Public
      Integrative pipeline for cell type deconvolution from bulk RNAseq using first and second generation methods
      R
      •
      Other
      •0•4•6•0•Updated Apr 2, 2026Apr 2, 2026

    • pipeML

      Public
      A flexible and modular machine learning framework designed to support leakage-free model training through custom cross-validation fold construction
      R
      •
      GNU General Public License v3.0
      •0•3•2•0•Updated Mar 30, 2026Mar 30, 2026

    • ABM_NLC-CLL

      Public
      Physicell model of NLC-CLL differentiation
      Jupyter Notebook
      •1•0•0•0•Updated Mar 28, 2026Mar 28, 2026

    • tysserand

      Public
      Fast reconstruction of spatial networks from bioimages.
      networkspatial-analysisnetwork-analysis
      networkspatial-analysisnetwork-analysisspatial-networkbioimage-analysis
      Python
      •
      GNU General Public License v3.0
      •6•26•3•1•Updated Mar 27, 2026Mar 27, 2026

    • .github

      Public
      0•0•0•0•Updated Mar 20, 2026Mar 20, 2026

    • SCIE-PANC.github.io

      Public
      Github Pages site for TRANSCAN Project
      SCSS
      •0•0•0•0•Updated Feb 20, 2026Feb 20, 2026

    • Gene_Ages_3D_Paper

      Public
      Exploring the relation between evolutionary gene age, gene expression and chromatin 3D structure in cancer
      R
      •0•0•0•0•Updated Jan 27, 2026Jan 27, 2026

    • CLL_GRN_paper

      Public
      Time-series RNA-Seq and data-driven network inference unveil dynamic cell phenotypes in Chronic Lymphocytic Leukaemia
      graphnetworktime-series-analysis
      graphnetworktime-series-analysisbulkrna-seq
      C
      •
      MIT License
      •1•5•0•0•Updated Jan 21, 2026Jan 21, 2026

    • multideconv_paper

      Public
      Repository containing the analysis and results for the multideconv paper
      R
      •0•0•1•0•Updated Nov 20, 2025Nov 20, 2025

    • TRANSDUCER

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Oct 14, 2025Oct 14, 2025

    • mosna

      Public
      MOSNA: multi-omics spatial network analysis
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Sep 26, 2025Sep 26, 2025

    • PhysiGym

      Public
      PhysiGym is a tool for applying reinforcement learning to PhysiCell
      Python
      •
      Other
      •4•0•0•0•Updated Sep 21, 2025Sep 21, 2025

    • LungPredict1_paper

      Public
      Profiling the Non-Small Cell Lung Cancer (NSCLC) microenvironment by integrating transcriptomics to uncover potential phenotypic profiles associated to patterns…
      R
      •0•3•0•0•Updated Nov 14, 2024Nov 14, 2024

    • LungPredict1

      Public
      Profiling the Non-Small Cell Lung Cancer (NSCLC) microenvironment by integrating transcriptomics to uncover potential phenotypic profiles associated to patterns…
      R
      •0•0•0•0•Updated Aug 16, 2024Aug 16, 2024

    • Spatial-Omics-Networks-Benchmark-

      Public
      Spatial Omics Networks Benchmark
      Jupyter Notebook
      •0•0•0•0•Updated Aug 2, 2024Aug 2, 2024

    • GEMDeCan_deconvolution

      Public
      Snakemake pipeline to perform immune cell type deconvolution in bulk RNAseq data using gene expression and methylation signatures.
      R
      •1•2•0•0•Updated May 24, 2024May 24, 2024

    • Alexis_Hucteau_Thesis_git

      Public
      HTML
      •1•0•0•0•Updated Mar 14, 2024Mar 14, 2024

    • GEMDeCan

      Public
      GEMDeCan: Gene expression and methylation based deconvolution for Cancer
      Python
      •3•6•0•0•Updated Mar 7, 2024Mar 7, 2024

    • GARDEN-NET

      Public
      Genome ARchitecture Data Epigenome and Nucleome - Network Exploration Tool (GARDEN-NET)
      TypeScript
      •
      GNU Affero General Public License v3.0
      •0•6•9•0•Updated May 19, 2023May 19, 2023

    • Agent-Based-Model-of-NLC-in-CLL

      Public
      An Agent-Based Model of Monocyte Differentiation into Tumor-Associated Macrophages in Chronic Lymphocytic Leukemia
      NetLogo
      •1•2•0•0•Updated Mar 29, 2023Mar 29, 2023

    • RepOri3D

      Public
      R
      •0•0•0•0•Updated Aug 22, 2022Aug 22, 2022

    • Pancreatic-Cancer-Spatial-Network-Analysis

      Public
      Pancreatic Cancer Network Reconstruction and Analysis
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 6, 2022Apr 6, 2022

    • verapancaldilab.github.io

      Public
      VeraPancaldiLab web
      CSS
      •
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Jan 17, 2020Jan 17, 2020

    • ChAseR_demo

      Public
      ChAseR demo
      HTML
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated Jan 16, 2020Jan 16, 2020

    • GARDEN-NET_backend

      Public
      Set of utilities and helpers for generating json networks in cytoscape.js json format from R dataframes to TSV format in https://github.com/VeraPancaldiLab/GARD…
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 16, 2019Dec 16, 2019

    • mg-process-chas

      Public
      mg-process-chas for ChAs
      Python
      •
      Apache License 2.0
      •1•0•0•0•Updated Nov 9, 2018Nov 9, 2018

    • Chromatin_Assortativity

      Public
      R
      •1•0•0•0•Updated Jun 27, 2018Jun 27, 2018

    • Heterosis-GRN-simulation

      Public
      R code of a gene regulatory network simulation of hybrid vigour
      R
      •1•1•0•0•Updated Sep 6, 2013Sep 6, 2013
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