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    32 repositories

    • SpatialBiologyHackathon2026

      Public
      Useful scripts for Spatial Biology Hackathon 2026 at VUMC
      R
      •
      MIT License
      •0•0•0•0•Updated Jan 20, 2026Jan 20, 2026

    • MSI-SEER

      Public
      Python
      •0•3•2•0•Updated Jul 19, 2024Jul 19, 2024

    • HE_IHC_HN_analysis

      Public
      Integrative Spatial Analysis of H&E and IHC Images Identifies Prognostic Immune Subtypes correlated with Progression Free Survival in HPV-Related Oropharyngeal …
      registrationihche
      registrationihchesegmentation-modelswsi-images
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •1•6•1•0•Updated Jul 8, 2024Jul 8, 2024

    • istar

      Public
      Python
      •
      GNU General Public License v3.0
      •31•0•0•0•Updated May 17, 2024May 17, 2024

    • GC_ICI_response_prediction

      Public
      Python
      •0•0•0•0•Updated Apr 7, 2024Apr 7, 2024

    • 3D_tissue_visualization

      Public
      Python
      •0•0•0•0•Updated Dec 18, 2023Dec 18, 2023

    • HT_img_reconstruction

      Public
      Python
      •0•0•0•0•Updated Nov 10, 2023Nov 10, 2023

    • Style_transfer_BF_HE

      Public
      CycleGAN based style transfer from BF image to HE image.
      Python
      •0•0•0•0•Updated Nov 10, 2023Nov 10, 2023

    • WSI_registration

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •1•2•0•0•Updated Sep 19, 2023Sep 19, 2023

    • test

      Public
      Python
      •0•0•0•0•Updated May 31, 2023May 31, 2023

    • tcga_stroma_prediction

      Public
      Python
      •0•2•0•0•Updated May 11, 2023May 11, 2023

    • AML_biomarkers

      Public
      R
      •0•2•0•0•Updated Feb 7, 2023Feb 7, 2023

    • wsitiler

      Public
      Tools for dividing pathology whole slide images into tiles and save them as individual files.
      Python
      •
      GNU General Public License v3.0
      •0•2•4•0•Updated Jan 19, 2023Jan 19, 2023

    • Stromal_ACTA2_ICI_Analysis

      Public
      R
      •0•1•0•0•Updated Oct 21, 2022Oct 21, 2022

    • Yonsei_gastric_cancer_32genes

      Public
      MATLAB
      •0•3•1•0•Updated Jun 15, 2022Jun 15, 2022

    • hwanglab_2021_tigitCarT

      Public
      TIGIT dysfunction role in CD19 CAR-T therapy for NHL
      R
      •0•0•0•0•Updated May 25, 2022May 25, 2022

    • 2022_multiomic_GC

      Public
      Multi-omics Reveals Microbiome, Host Gene Expression, and Immune Landscape in Gastric Carcinogenesis
      R
      •2•0•0•0•Updated Feb 7, 2022Feb 7, 2022

    • DGP_RF_WSL_TripletLoss

      Public
      Python
      •0•4•0•0•Updated Oct 15, 2021Oct 15, 2021

    • Deep_learning_WSI_tutorial

      Public
      Jupyter Notebook
      •
      MIT License
      •3•3•0•0•Updated Jun 25, 2021Jun 25, 2021

    • apa_atingLab2019

      Public
      DNA methylation regulates alternative polyadenylation via CTCF and the cohesin complex (2019 paper submission)
      R
      •3•5•0•0•Updated Jan 16, 2021Jan 16, 2021

    • tcga_tmb_prediction

      Public
      TCGA BLCA tmb prediction by Hongming Xu
      MATLAB
      •4•13•0•0•Updated Nov 1, 2020Nov 1, 2020

    • TILs_Analysis

      Public
      Pan-cancer tils analysis study by Hongming Xu
      Python
      •4•14•1•0•Updated Oct 29, 2020Oct 29, 2020

    • pathology_analysis_examples

      Public
      tutorials for wsi analysis by Hongming Xu
      Python
      •0•7•0•0•Updated Sep 23, 2020Sep 23, 2020

    • BayesianSNMTF

      Public
      MATLAB
      •0•0•0•0•Updated May 25, 2020May 25, 2020

    • singlecell_tutorial

      Public
      single cell sequencing analysis tutorial
      HTML
      •6•18•0•0•Updated Jan 15, 2020Jan 15, 2020

    • tcga-prad-cslbp

      Public
      TCGA prostate cancer Gleason score prediction using completed and statistical local binary patterns (Matlab/Python programs)
      MATLAB
      •4•5•0•0•Updated Sep 20, 2019Sep 20, 2019

    • CRISPinatoR_database

      Public
      Database generating source codes for CRISPinatoR
      C
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 21, 2019May 21, 2019

    • divine

      Public
      Divine: Prioritizing Genes for Rare Mendelian Disease in Whole Exome Sequencing Data
      Python
      •1•13•3•1•Updated Apr 18, 2019Apr 18, 2019

    • NTriPath

      Public
      NTriPath Matlab code
      MATLAB
      •
      MIT License
      •3•6•2•0•Updated Oct 22, 2018Oct 22, 2018

    • rnaseq_workshop

      Public
      Cleveland Clinic Bioinformatics Workshop for RNA-Seq data analysis
      4•7•0•0•Updated Jul 20, 2018Jul 20, 2018
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