Software

CANCER SUBTYPING

• PINSPlus: subtyping and big data analysis
  – CRAN: https://CRAN.R-project.org/package=PINSPlus
• SMRT: subtyping and big data analysis
  – Web application: https://tinnguyen-lab.com/software/SMRT/
  – CRAN: https://CRAN.R-project.org/package=PINSPlus

PATHWAY & INTEGRATION

• CPA: Consensus pathway analysis and interactive pathway visualization
  – Tutorial: https://storage.googleapis.com/nosi-gcloud-course/html/intro.html
  

SINGLE-CELL ANALYSIS

• scCAN: single-cell clustering using autoencoder and network fusion
  – Publication: https://www.nature.com/articles/s41598-022-14218-6
  – CRAN: https://CRAN.R-project.org/package=scCAN
  

• scISR: A novel method for single-cell data imputation using subspace regression
  – Publication: https://www.nature.com/articles/s41598-022-06500-4
  – CRAN: https://cran.r-project.org/package=scISR
  

• scDHA: Fast and precise single-cell data analysis using a hierarchical autoencoder
  – Publication: https://www.nature.com/articles/s41467-021-21312-2
  – CRAN: https://CRAN.R-project.org/package=scDHA