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    49 repositories

    • tgif

      Public
      Tree-Guided Integrated Factorization (TGIF)
      C
      •0•2•1•0•Updated Jan 2, 2025Jan 2, 2025

    • scMTNI

      Public
      C
      •4•23•4•1•Updated Dec 31, 2024Dec 31, 2024

    • SCOTCH

      Public
      A pytorch enabled implementation of the regularized non-negative matrix tri-factorization algorithm. This is Nvidia GPU compatible.
      Jupyter Notebook
      •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

    • new-member

      Public
      References and resources for new members
      0•1•0•0•Updated Sep 11, 2024Sep 11, 2024

    • pancreatic_cell_grns

      Public
      Repository for analysis done for XBP1 paper
      Python
      •0•0•0•0•Updated Aug 28, 2024Aug 28, 2024

    • roy-lab.github.io

      Public
      0•0•0•0•Updated Jun 2, 2024Jun 2, 2024

    • Muscari

      Public
      MUSCARI (Multi-task Spectral Clustering AlgoRIthm)
      C
      •0•1•0•0•Updated Jun 2, 2024Jun 2, 2024

    • grinch

      Public
      GRiNCH: Graph-Regularized NMF and Clustering for Hi-C
      C
      •1•9•2•0•Updated Mar 15, 2024Mar 15, 2024

    • MERLIN-VIZ

      Public
      A visualization toolset for MERLIN Networks. Allows for direct user interaction.
      network-inferencenetwork-visualization
      R
      •0•0•0•0•Updated Mar 12, 2024Mar 12, 2024

    • Escarole

      Public
      Expression State Clustering on Lineages (Escarole)
      C
      •1•1•2•0•Updated Jan 30, 2024Jan 30, 2024

    • compnetbiocourse

      Public
      This repository has homework and assignment related files for the Computational Network Biology course BMI/CS 775.
      Jupyter Notebook
      •0•0•0•0•Updated Nov 16, 2023Nov 16, 2023

    • Tutorial_for_Aboretum-based_DE_geneset_analysis

      Public
      A tutorial which includes Arboretum & findTransitionGenesets with an example dataset.
      C
      •0•0•0•0•Updated Nov 10, 2023Nov 10, 2023

    • graph-representation-learning

      Public
      Comparison of various node embedding algorithms on node classification downstream task
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 10, 2023Sep 10, 2023

    • merlin-preprocess

      Public
      Preprocessing methods for MERLIN.
      HTML
      •0•0•0•0•Updated May 5, 2023May 5, 2023

    • Arboretum2.0

      Public
      The Arboretum 2.0 is the next release of the original code of Arboretum. It makes running Arboretum easier by taking care of initial cluster assignments.
      clustering
      C
      •1•2•0•0•Updated May 2, 2023May 2, 2023

    • merlin-auxillary

      Public
      Downstream analysis for MERLIN inferred networks
      C
      •1•0•0•1•Updated Apr 19, 2023Apr 19, 2023

    • Roadmap_RegulatoryVariation

      Public
      C
      •0•4•0•0•Updated Jan 4, 2023Jan 4, 2023

    • scRNAseq_NetInference

      Public
      Jupyter Notebook
      •3•4•3•0•Updated Nov 3, 2022Nov 3, 2022

    • merlin-p_self_checkpoint

      Public
      MERLIN-P with self checkpointing for Condor
      C
      •0•0•0•0•Updated Jul 9, 2022Jul 9, 2022

    • clade-specific_gene_sets

      Public
      Scripts for selecting clade-specific gene sets from Arboretum result matrix
      C
      •0•0•0•0•Updated Jun 21, 2022Jun 21, 2022

    • maize_autophagy

      Public
      C
      •0•0•0•0•Updated May 2, 2022May 2, 2022

    • subcluster_analysis

      Public
      A repository of results from the Arboretum analysis to identify complex gene expression patterns in subpopulation subclusters.
      HTML
      •
      MIT License
      •0•0•0•0•Updated Apr 29, 2022Apr 29, 2022

    • sc_ConsensusClustering

      Public
      Scripts for unbiased clustering and consensus clustering
      MATLAB
      •
      MIT License
      •0•0•0•0•Updated Apr 29, 2022Apr 29, 2022

    • afum_prior_net_constr

      Public
      Files used for the prior network construction of Aspergillus fumigatus
      Python
      •1•0•0•0•Updated Apr 4, 2022Apr 4, 2022

    • mvnmf

      Public
      C
      •0•0•0•0•Updated Feb 14, 2022Feb 14, 2022

    • drmn

      Public
      DRMN with multi-task learning regression
      C
      •1•5•1•0•Updated Jan 28, 2022Jan 28, 2022

    • merlin-p_inferred_networks

      Public
      1•1•0•0•Updated Dec 10, 2021Dec 10, 2021

    • graph_louvain_clustering

      Public
      Python
      •1•0•0•1•Updated Oct 20, 2021Oct 20, 2021

    • drmn_utils

      Public
      Ancillary utilities for DRMN. Input processing and interpreting results.
      C
      •0•0•0•0•Updated Jul 27, 2021Jul 27, 2021

    • utils

      Public
      Roy lab in-house utilities
      C
      •0•0•0•0•Updated Jun 21, 2021Jun 21, 2021