Software

CANCER SUBTYPING

• SCFA: subtyping and risk prediction
  – GitHub: https://github.com/duct317/SCFA
  – Bioconductor: https://bioconductor.org/packages/SCFA/
• PINSPlus: subtyping and big data analysis
  – CRAN: https://CRAN.R-project.org/package=PINSPlus
• SMRT: subtyping and big data analysis
  – Web application: https://smrt.tinnguyen-lab.com/
  – CRAN: https://CRAN.R-project.org/package=PINSPlus

DATABASE

• FAT-PTM: examining post-translational modification in plants
  – Web application: https://fat-ptm.tinnguyen-lab.com
• ThYme: A comprehensive database of the Thioester-active enzYmes
  – Web application: https://thyme.engr.unr.edu/v2.0/

PATHWAY & INTEGRATION

• CPA: Consensus pathway analysis and interactive pathway visualization
  – Publication: https://academic.oup.com/nar/article/49/W1/W114/6284183
  – Web application: https://cpa.tinnguyen-lab.com
  

• RCPA: An Open-Source R Package for Data Processing, Differential Analysis, Consensus Pathway Analysis, and Visualization
  – Publication: https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpz1.1036
  

  • CRAN: https://CRAN.R-project.org/package=RCPA
    

• CCPA: cloud-based, self-learning modules for consensus pathway analysis using GO, KEGG and Reactome
  – Publication: https://academic.oup.com/bib/article/25/Supplement_1/bbae222/7718483
  

  • Tutorial: https://github.com/NIGMS/Consensus-Pathway-Analysis-in-the-Cloud
    

• Intelligent Platform for Systems-level Analysis
  – Web application: https://ipsa.tinnguyen-lab.com
  – Tutorial: https://tutorial-aipa.tinnguyen-lab.com/
  – Video Tutorial: https://youtu.be/LF7ryDqFVDc
  

• BLMA: a suit of tools for bi-level meta-analysis
  – Bioconductor: https://bioconductor.org/packages/release/bioc/html/BLMA.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
  

• DeconBenchmark: A package provides a common interface to run 50 cellular deconvolution methods
  – Publication: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae267/7645775
  – GitHub: https://github.com/tinnlab/DeconBenchmark
  

• CytoAnalyst: A web platform facilitates comprehensive single cell RNA sequencing analysis
  – Publication: https://www.nature.com/articles/s41598-025-14398-x
  – GitHub: https://cytoanalyst.tinnguyen-lab.com/