Repositories list

• 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 procedure.

  R

  •1•1•0•0•Updated Jan 22, 2025Jan 22, 2025

• CNAfingerprint

  Public
  R

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 6, 2025Jan 6, 2025

• CNAfingerprint_demo

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

• CNAfingerprint_mCRC

  Public
  CNAfingerprint, A biomarker for oxaliplatin-based chemotherapy response prediction in mCRC

  0•0•0•0•Updated Dec 31, 2024Dec 31, 2024

• TcrDesign

  Public
  T Cell Receptor Design Through Deep Learning Methods

  Python

  •0•1•0•0•Updated Dec 25, 2024Dec 25, 2024

• CancerBiology

  Public
  Support materials for 《Cancer Biology》，Shanghaitech University

  JavaScript

  •0•0•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•0•0•Updated Sep 2, 2024Sep 2, 2024

• DeepMeta

  Public
  Precise metabolic dependencies of cancer through deep learning

  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Jun 27, 2024Jun 27, 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+ 1workshop

  HTML

  •50•188•2•0•Updated Apr 17, 2024Apr 17, 2024

• MethyDeep

  Public
  Python

  •1•3•0•0•Updated Jul 26, 2023Jul 26, 2023

• Neodb

  Public
  Shiny Web Server and Database for Neoantigen discovery

  Jupyter Notebook

  •

  MIT License

  •0•3•2•0•Updated Jun 25, 2023Jun 25, 2023

• TLimmuno2

  Public
  TLimmuno2: predicting MHC class II antigen immunogenicity through transfer learning

  deep-learning

  HTML

  •2•8•0•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•21•4•0•Updated Feb 17, 2023Feb 17, 2023

• HRDCNA

  Public
  A robust homologous recombination deficiency predictor based on copy number alteration features

  R

  •

  Other

  •0•2•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+ 1immunoediting

  HTML

  •

  Apache License 2.0

  •1•11•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•5•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

  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

  biomarker-discoveryimmunotherapymanuscript+ 3reproducible-analysisanalysis-reporttumor-immunogenicity

  R

  •

  Apache License 2.0

  •16•31•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+ 2sigmineralteration-signature

  R

  •7•12•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

• CDC20

  Public
  R

  •1•1•1•0•Updated Apr 20, 2020Apr 20, 2020

• XSLab-docs

  Public
  上科大刘雪松课题组基因组学分析传承与分享知识库

  10•13•3•0•Updated Feb 21, 2020Feb 21, 2020