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    45 repositories

    • CNAfingerprint

      Public
      CNAfingerprint
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 20, 2026Jan 20, 2026

    • DeepMeta

      Public
      Precise metabolic dependencies of cancer through deep learning
      Jupyter Notebook
      •
      MIT License
      •2•5•0•0•Updated Jan 7, 2026Jan 7, 2026

    • CNAfingerprint_mCRC

      Public
      CNAfingerprint, A biomarker for oxaliplatin-based chemotherapy response prediction in mCRC
      0•1•0•0•Updated Nov 20, 2025Nov 20, 2025

    • Neodb

      Public
      Shiny Web Server and Database for Neoantigen discovery
      Jupyter Notebook
      •
      MIT License
      •0•4•0•0•Updated Aug 18, 2025Aug 18, 2025

    • single-cell-CNA-signature

      Public
      This repository provides the analysis reports, code and data for readers who are insterest in this project and make it easier to reproduce the whole analysis pr…
      R
      •1•3•0•0•Updated Aug 2, 2025Aug 2, 2025

    • AbTcrAI

      Public
      AbTcrAI web
      HTML
      •0•0•0•0•Updated May 29, 2025May 29, 2025

    • CNV_lcWGS_benchmark

      Public
      0•0•0•0•Updated Apr 9, 2025Apr 9, 2025

    • CNAfingerprint_demo

      Public
      0•0•0•0•Updated Jan 1, 2025Jan 1, 2025

    • TcrDesign

      Public
      T Cell Receptor Design Through Deep Learning Methods
      Python
      •0•2•0•0•Updated Dec 25, 2024Dec 25, 2024

    • CancerBiology

      Public
      Support materials for 《Cancer Biology》，Shanghaitech University
      JavaScript
      •0•1•0•0•Updated Dec 23, 2024Dec 23, 2024

    • Pep2TCR

      Public
      Pep2TCR: a novel deep learning method for CD4 TCR specificity prediction
      Python
      •
      MIT License
      •0•1•0•0•Updated Sep 9, 2024Sep 9, 2024

    • TCfinder

      Public
      R
      •
      Other
      •2•9•1•0•Updated Sep 2, 2024Sep 2, 2024

    • hypoxia_target

      Public
      Deep learning reveals the metabolic vulnerability of hypoxic tumor cells and the critical function of FLAD1 mediated tumor hypoxia adaption
      Jupyter Notebook
      •0•2•0•0•Updated Apr 19, 2024Apr 19, 2024

    • Workshop

      Public
      课题组每周研讨会
      data-sciencebioinformaticsr
      data-sciencebioinformaticsrworkshop
      HTML
      •52•206•2•0•Updated Apr 17, 2024Apr 17, 2024

    • MethyDeep

      Public
      Python
      •1•4•0•0•Updated Jul 26, 2023Jul 26, 2023

    • TLimmuno2

      Public
      TLimmuno2: predicting MHC class II antigen immunogenicity through transfer learning
      deep-learning
      deep-learning
      HTML
      •6•13•2•0•Updated Jun 19, 2023Jun 19, 2023

    • InterpretationAnalysisHRDCNA

      Public
      An interpretation analysis of copy number alteration features in pan-cancer homologous recombination deficiency prediction and biology
      HTML
      •
      MIT License
      •1•2•0•0•Updated Apr 23, 2023Apr 23, 2023

    • Seq2Neo

      Public
      Seq2Neo: a comprehensive pipeline for cancer neoantigen immunogenicity prediction
      Python
      •
      Academic Free License v3.0
      •2•24•4•0•Updated Feb 17, 2023Feb 17, 2023

    • HRDCNA

      Public
      A robust homologous recombination deficiency predictor based on copy number alteration features
      R
      •
      Other
      •1•3•0•0•Updated Nov 16, 2022Nov 16, 2022

    • Immunoediting_response_letter_CR

      Public
      R
      •0•1•0•0•Updated Oct 10, 2022Oct 10, 2022

    • Immunoediting

      Public
      Pan-cancer quantification of neoantigen-mediated immunoediting in cancer evolution
      cancer-genomicsimmunotherapyanalysis-report
      cancer-genomicsimmunotherapyanalysis-reportimmunoediting
      HTML
      •
      Apache License 2.0
      •2•14•0•0•Updated May 4, 2022May 4, 2022

    • ecDNA_immune

      Public
      Extrachromosomal DNA is associated with decreased immune cell infiltration and antigen presentation, represents a potential cancer immune evasion mechanism
      HTML
      •
      MIT License
      •3•8•0•0•Updated Mar 5, 2022Mar 5, 2022

    • Pan-cancer_CNA_signature

      Public
      https://xsliulab.github.io/Pan-cancer_CNA_signature/
      R
      •
      MIT License
      •2•6•0•0•Updated Jan 27, 2022Jan 27, 2022

    • FoLST2021-Immunediting-Poster

      Public
      HTML
      •0•0•0•0•Updated Dec 16, 2021Dec 16, 2021

    • FoLST2021-PancancerCNAsig-Poster

      Public
      A poster showing Pancancer CNA signature project at FoLST2021, ShanghaiTech University.https://xsliulab.github.io/FoLST2021-PancancerCNAsig-Poster/
      postersignaturefolst2021
      postersignaturefolst2021
      HTML
      •0•1•0•0•Updated Dec 14, 2021Dec 14, 2021

    • tumor-immunogenicity-score

      Public
      TIGS (Tumor Immunogenicity Score) project https://doi.org/10.7554/eLife.49020
      manuscriptbiomarker-discoveryimmunotherapy
      manuscriptbiomarker-discoveryimmunotherapyreproducible-analysisanalysis-reporttumor-immunogenicity
      R
      •
      Apache License 2.0
      •16•33•0•0•Updated Sep 16, 2021Sep 16, 2021

    • PC_CNA_signature

      Public
      Prostate Cancer Alteration Signature Analysis https://xsliulab.github.io/PC_CNA_signature/
      rmarkdowncancer-genomicsmutational-signatures
      rmarkdowncancer-genomicsmutational-signaturessigmineralteration-signature
      R
      •7•13•0•0•Updated May 17, 2021May 17, 2021

    • Noncoding-code-2020

      Public
      CDC20 noncoding project
      R
      •
      Apache License 2.0
      •4•7•0•0•Updated May 23, 2020May 23, 2020

    • PromoterMutSpot

      Public
      R
      •1•1•0•0•Updated May 21, 2020May 21, 2020

    • noncoding-cdc20

      Public
      R
      •
      Apache License 2.0
      •2•1•1•1•Updated Apr 27, 2020Apr 27, 2020
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