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@rsinghlab Singh Lab @ Brown

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    26 repositories

    • pyaging

      Public
      A Python-based compendium of GPU-optimized aging clocks.
      clocktorchagingbiomarkers
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•87•0•0•Updated Mar 8, 2025Mar 8, 2025

    • Shape-Blind

      Public
      Jupyter Notebook
      •0•4•1•0•Updated Mar 4, 2025Mar 4, 2025

    • STING

      Public
      Spatial Transcriptomics cluster Inference with Nested GNNs
      Python
      •0•0•0•0•Updated Mar 3, 2025Mar 3, 2025

    • K-Paths

      Public
      Official Implementation of K-Paths: Reasoning over Graph Paths for Drug Repurposing and Drug Interaction Prediction.
      knowledge-graphreasoninggraph-neural-networkslarge-language-models
      Python
      •0•10•0•0•Updated Feb 15, 2025Feb 15, 2025

    • TimeFlies

      Public
      Jupyter Notebook
      •0•2•0•0•Updated Feb 6, 2025Feb 6, 2025

    • ML_epigenetic_features_glioblastoma

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Feb 4, 2025Feb 4, 2025

    • HistoneClocks

      Public
      This repository contains the code and data to reproduce the results of our paper entitled "Histone mark age of human tissues and cells".
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Jan 3, 2025Jan 3, 2025

    • scMultiNODE

      Public
      scMultiNODE: Temporal Single-Cell Data Integration across Unaligned Modalities
      Python
      •
      MIT License
      •0•1•0•0•Updated Nov 1, 2024Nov 1, 2024

    • QZERO

      Public
      Retrieval Augmented Zero-Shot Text Classification
      Python
      •0•5•0•0•Updated Nov 1, 2024Nov 1, 2024

    • scNODE

      Public
      scNODE: Generative Model for Temporal Single Cell Transcriptomic Data Prediction
      Jupyter Notebook
      •
      MIT License
      •2•19•2•0•Updated Oct 11, 2024Oct 11, 2024

    • OvO

      Public
      Jupyter Notebook
      •
      MIT License
      •1•11•0•0•Updated Sep 30, 2024Sep 30, 2024

    • GC-MERGE

      Public
      This is the repository for the long-range interaction GCNN for predicting gene expression for the Singh Lab.
      Python
      •
      MIT License
      •1•5•3•0•Updated Sep 11, 2024Sep 11, 2024

    • scGrapHiC

      Public
      A graph deconvolution approach to predict Hi-C contact map from pseudo-bulk scRNA-seq.
      Python
      •0•5•1•0•Updated Aug 24, 2024Aug 24, 2024

    • AltumAge

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •9•29•1•0•Updated Aug 3, 2024Aug 3, 2024

    • SCOT

      Public
      Gromov-Wasserstein based optimal transport for aligning single-cell multi-omics data
      Jupyter Notebook
      •
      MIT License
      •17•69•5•1•Updated Jan 25, 2024Jan 25, 2024

    • scRNAseq_Coexpression_Benchmark

      Public
      A benchmark of existing gene co-expression estimator on scRNA-seq data.
      HTML
      •
      MIT License
      •0•2•1•0•Updated Oct 11, 2023Oct 11, 2023

    • CliniqIR

      Public
      Code for the paper: Unsupervised Diagnostic Decision Support via Information Retrieval
      Python
      •1•2•0•0•Updated Oct 9, 2023Oct 9, 2023

    • GrapHiC

      Public
      A graph neural network based approach to impute missing Hi-C reads.
      deep-learningpytorch
      Python
      •0•9•1•0•Updated Jul 28, 2023Jul 28, 2023

    • gnn_microscopy_segment

      Public
      Memory Efficient Semantic Segmentation of Large Microscopy Images Using Graph-based Neural Networks
      Python
      •0•6•1•0•Updated Jul 14, 2023Jul 14, 2023

    • SCOOTR

      Public
      Single-cell CO-Optimal TRansport for jointly aligning cells and genomic features of single-cell multi-omic datasets
      Python
      •1•2•1•0•Updated Jul 13, 2023Jul 13, 2023

    • Hi-CY

      Public
      Python
      •0•0•0•0•Updated May 1, 2023May 1, 2023

    • MADDi

      Public
      This repository is for the Multimodal Alzheimer’s Disease Diagnosis framework (MADDi).
      Jupyter Notebook
      •
      MIT License
      •18•93•2•0•Updated Apr 26, 2023Apr 26, 2023

    • GNN-Tumor-Seg

      Public
      Using Graph Neural Networks to Segment MRIs of Brain Tumors
      Python
      •4•22•0•0•Updated Aug 13, 2022Aug 13, 2022

    • ChromAge

      Public
      Private repository for the chromatin age prediction project developed by Lucas and Haider.
      Python
      •0•1•0•0•Updated Apr 27, 2022Apr 27, 2022

    • CoRNN

      Public
      Compartment prediction using Recurrent Neural Network
      Python
      •1•2•0•0•Updated Mar 15, 2022Mar 15, 2022

    • scMultiOmics_Datasets

      Public
      Datasets for the scGRN project
      0•0•0•0•Updated Dec 6, 2021Dec 6, 2021