Repositories list

• MSI-SEER

  Public
  Python

  •0•0•0•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 Squamous Cell Carcinoma

  registrationihche+ 2segmentation-modelswsi-images

  Jupyter Notebook

  •

  GNU General Public License v2.0

  •1•5•1•0•Updated Jul 8, 2024Jul 8, 2024

• istar

  Public
  Python

  •

  GNU General Public License v3.0

  •16•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

• WSI_registration

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •0•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•2•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

  •1•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

  •2•3•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

  •2•13•0•0•Updated Oct 29, 2020Oct 29, 2020

• pathology_analysis_examples

  Public
  tutorials for wsi analysis by Hongming Xu

  Python

  •0•5•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

  •7•16•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•12•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•6•0•0•Updated Jul 20, 2018Jul 20, 2018

• binf_workshop_2018_01

  Public
  Cleveland Clinic Bioinformatics Workshop January 2018

  Shell

  •2•1•0•0•Updated Feb 2, 2018Feb 2, 2018

• OptiType

  Public
  Precision HLA typing from next-generation sequencing data

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •77•0•0•0•Updated Dec 2, 2017Dec 2, 2017