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    24 repositories

    • Adebari_Glioma_scripts

      Public
      Scripts used to replicate the results for the Adebari et al paper comparing sex differences in glioblastomas and low-grade gliomas.
      R
      •0•1•0•0•Updated Apr 29, 2026Apr 29, 2026

    • UNAGI_paper_scripts

      Public
      Scripts used to replicate the results in the UNAGI paper
      R
      •0•0•0•0•Updated Mar 20, 2026Mar 20, 2026

    • LOY_lung_cancer

      Public
      Companion repository for our study on loss of Y chromosome (LOY) in lung cancer
      R
      •1•1•0•0•Updated Feb 9, 2026Feb 9, 2026

    • tcga-data-nf

      Public
      Workflow to download and prepare TCGA data
      HTML
      •
      GNU General Public License v3.0
      •4•3•2•1•Updated Feb 4, 2026Feb 4, 2026

    • FERRET

      Public
      Framework to Evaluate Robustness in Regulatory Networks Using Heterogeneous Cell Types
      R
      •0•0•0•0•Updated Jan 20, 2026Jan 20, 2026

    • grand

      Public
      GRAND database of gene regulatory networks.
      gene-regulatory-network
      gene-regulatory-network
      JavaScript
      •2•6•4•0•Updated Oct 23, 2025Oct 23, 2025

    • tcga-data-supplement

      Public
      supplementary notebooks and configuration files for the tcga-data-manuscript
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Aug 14, 2025Aug 14, 2025

    • NetworkDataCompanion

      Public
      An R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo
      HTML
      •
      GNU General Public License v3.0
      •0•8•10•0•Updated Jun 30, 2025Jun 30, 2025

    • Waelchli_Glioma_scripts

      Public
      Scripts used in analysis as part of the collaboration between Thomas Waelchli and our group.
      R
      •0•0•0•0•Updated Feb 26, 2025Feb 26, 2025

    • BLOBFISH_paper_scripts

      Public
      These are the scripts needed to replicate the results in the BLOBFISH paper.
      R
      •0•0•0•0•Updated Feb 20, 2025Feb 20, 2025

    • cobra-experiments

      Public
      Experiments for the paper "Higher-order correction of persistent batch effects in correlation networks".
      R
      •
      MIT License
      •0•4•0•0•Updated Nov 12, 2024Nov 12, 2024

    • QuackenbushLab.github.io

      Public
      Landing page of the network science lab at Harvard Biostats
      HTML
      •
      MIT License
      •0•0•0•0•Updated Oct 30, 2024Oct 30, 2024

    • DASH

      Public
      DASH (Domain Aware Sparsity Heuristic) is a neural network pruning strategy that leverages domain-knowledge to obtain *meaningfully sparse* models.
      Python
      •
      MIT License
      •1•4•0•0•Updated Jun 1, 2024Jun 1, 2024

    • phoenix

      Public
      PHOENIX: a tool to infer biologically informed NeuralODEs describing genome-wide regulatory dynamics
      Python
      •
      MIT License
      •6•20•2•0•Updated May 8, 2024May 8, 2024

    • yarn

      Public
      YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization
      R
      •2•13•5•0•Updated Mar 4, 2024Mar 4, 2024

    • neural_ODE

      Public
      project: replacing the use of RNNs in gene-regulatory network prediction, with ODEs.
      Python
      •4•3•0•0•Updated Mar 1, 2024Mar 1, 2024

    • gpuzoo

      Public
      Benchmarks of the gpuZoo implementations.
      systems-biologygpu-computinggene-regulatory-network
      systems-biologygpu-computinggene-regulatory-network
      MATLAB
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 10, 2022Mar 10, 2022

    • MONSTER

      Public
      R
      •2•2•0•0•Updated Oct 15, 2020Oct 15, 2020

    • FENRIR

      Public
      RNA-seq pipeline to detect viral reads
      Shell
      •2•7•0•0•Updated Apr 14, 2020Apr 14, 2020

    • pypanda

      Public
      Python implementation of PANDA and LIONESS
      pythonbiologynetwork
      pythonbiologynetworkpandalioness
      Python
      •9•6•0•0•Updated Nov 7, 2019Nov 7, 2019

    • matlab-panda

      Public
      MATLAB implementation of PANDA & LIONESS algorithms
      biologynetworkmatlab
      biologynetworkmatlabpandalioness
      MATLAB
      •4•4•0•0•Updated Jul 10, 2019Jul 10, 2019

    • pandaR

      Public
      This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/pandaR.html Bug Reports: https…
      R
      •2•4•0•0•Updated Feb 9, 2017Feb 9, 2017

    • normFigures

      Public
      Scripts to preprocess entire GTEx dataset and produce all rough figures
      R
      •1•2•0•0•Updated Sep 13, 2016Sep 13, 2016

    • devbrim

      Public
      Modify bipartite modularity maximization algorithm
      R
      •0•0•0•0•Updated Sep 10, 2015Sep 10, 2015
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