Single-Cell Decomposition using Hierarchical Autoencoder R package scDHA version 1.2.3 Provides a fast and accurate pipeline for single-cell analyses. The 'scDHA' software package can perform clustering, dimension reduction and visualization, classification, and time-trajectory inference on single-cell data (Tran et.al. (2021) <DOI:10.1038/s41467-021-21312-2>). Software Depends: R (>= 3.4) Imports: matrixStats, foreach, doParallel, igraph, Matrix, uwot, cluster, Rcpp, RcppParallel, RcppAnnoy, methods, torch (>= 0.3.0), RhpcBLASctl, coro LinkingTo: Rcpp, RcppArmadillo, RcppParallel, RcppAnnoy Suggests: testthat, knitr, mclust Ha Nguyen <hvn0006@auburn.edu> Comprehensive R Archive Network (CRAN) Ha Nguyen [cre], Duc Tran [aut], Tin Nguyen [fnd], Hao Chen [ctb] GPL-3 2025-09-23 application/tgz https://CRAN.R-project.org/package=scDHA doi:10.32614/CRAN.package.scDHA