Software | Bioinformatics Lab

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

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/

CPA: Consensus pathway analysis and interactive pathway visualization
– Web application: https://cpa.tinnguyen-lab.com
– CRAN: https://CRAN.R-project.org/package=RCPA
– Tutorial: https://storage.googleapis.com/nosi-gcloud-course/html/intro.html
AIPA: AI-Powered Pathway Analysis and Biological Insights
– Web application: https://aipa.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

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