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    23 repositories

    • sisana

      Public
      Single Sample Network Analysis
      Python
      •
      MIT License
      •2•1•3•0•Updated Apr 23, 2026Apr 23, 2026

    • SCORPION

      Public
      Single Cell Oriented Reconstruction of PANDA-based Individually Optimized Networks
      transcription-factorstranscriptomicssingle-cell
      transcription-factorstranscriptomicssingle-cellprotein-protein-interactiongene-regulatory-networkcell-type-specificcomparative-edge-analysispopulation-comparison
      R
      •
      GNU General Public License v3.0
      •4•27•1•0•Updated Apr 3, 2026Apr 3, 2026

    • sponge

      Public
      Python package to generate prior gene regulatory networks.
      transcription-factorsgene-regulatory-network
      transcription-factorsgene-regulatory-network
      Python
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Apr 1, 2026Apr 1, 2026

    • pySCORPION

      Public
      Single Cell Oriented Reconstruction of PANDA-based Individually Optimized Networks
      transcription-factorstranscriptomicssingle-cell
      transcription-factorstranscriptomicssingle-cellprotein-protein-interactiongene-regulatory-networkcell-type-specificcomparative-edge-analysispopulation-comparison
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 4, 2026Mar 4, 2026

    • MARMOT

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 9, 2026Feb 9, 2026

    • multi-omics-course

      Public
      Repository for the multi-omics course
      HTML
      •
      MIT License
      •0•3•0•0•Updated Nov 11, 2025Nov 11, 2025

    • JDRnet

      Public
      This is a repository for reproducing the analysis in the paper: *title + doi*
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 29, 2025Oct 29, 2025

    • PANGOLIN

      Public
      this includes the pan-cancer analysis of gene regulatory landscape
      R
      •
      MIT License
      •1•0•0•0•Updated Oct 3, 2025Oct 3, 2025

    • CAVACHON

      Public
      Cell cluster Analysis with Variational Autoencoder using Conditional Hierarchy Of latent representioN
      Python
      •
      MIT License
      •2•4•0•1•Updated Apr 23, 2024Apr 23, 2024

    • PORCUPINE

      Public
      R
      •
      MIT License
      •1•2•0•0•Updated Jul 6, 2023Jul 6, 2023

    • HiC_networks

      Public
      Pipeline to convert Hi-C into networks, and perform network analysis on the 3D genome. Code developed by Gabriel Stav
      Python
      •1•0•0•0•Updated Jun 23, 2023Jun 23, 2023

    • PySNAIL

      Public
      Smooth-quantile Normalization Adaptation for Inference of co-expression Links
      bioinformaticsrna-seqnormalization
      bioinformaticsrna-seqnormalization
      Python
      •
      MIT License
      •1•16•0•0•Updated May 16, 2023May 16, 2023

    • BiHiDef

      Public
      Bipartite adaptation of HiDeF using BRIM
      Python
      •1•0•0•0•Updated Aug 16, 2022Aug 16, 2022

    • netZooPy

      Public
      netZooPy is a network biology package implemented in Python.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •38•0•0•0•Updated Jul 7, 2022Jul 7, 2022

    • phcancer

      Public
      Persistent homology on Lioness
      Python
      •1•1•0•0•Updated Jun 29, 2022Jun 29, 2022

    • retriever

      Public
      Generate Robust Disease-Specific Response Signatures from the LINCS-L1000 Data
      R
      •1•16•0•0•Updated Jan 21, 2022Jan 21, 2022

    • LIONESS_StarProtocols

      Public
      Code to support the LIONESS STAR Protocol
      MATLAB
      •
      MIT License
      •1•0•0•0•Updated Jun 4, 2021Jun 4, 2021

    • lionessR

      Public
      Single sample network reconstruction in R
      R
      •
      Other
      •6•7•0•0•Updated Dec 8, 2020Dec 8, 2020

    • PUMA

      Public
      PUMA: PANDA Using MicroRNA Associations
      C
      •
      GNU General Public License v2.0
      •4•1•0•0•Updated Jun 9, 2020Jun 9, 2020

    • PyPuma

      Public
      Python implementation of PUMA
      Python
      •2•1•0•0•Updated Dec 18, 2019Dec 18, 2019

    • pysambar

      Public
      SAMBAR (Subtyping Agglomerated Mutations By Annotation Relations) python implementation
      Python
      •1•0•0•0•Updated Aug 21, 2019Aug 21, 2019

    • pypanda

      Public
      Python implementation of PANDA and LIONESS
      Python
      •9•0•0•0•Updated Aug 16, 2019Aug 16, 2019

    • SAMBAR

      Public
      R package SAMBAR
      R
      •2•0•0•0•Updated Jul 4, 2019Jul 4, 2019
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