scTEP: Single-Cell Trajectory Inference using Ensemble Pseudotimes

A single-cell trajectory inference method using 'Autoencoder' and Minimum Spanning Tree (MST) from high dimensional 'scRNA-Seq' data. The software run clustering methods six times using 'scDHA' with the number of clusters set from 6 to 10. Then, the 'scTEP' calculates pseudotime based on multiple clustering results. Lastly, the 'scTEP' generates trajectory using MST algorithm and fine-tunes it according to the pseudotime of clusters.

Version: 0.1.0
Depends: R (≥ 3.6.0)
Imports: stats, dplyr, igraph, scDHA, foreach, BiocGenerics, Matrix, SummarizedExperiment, doParallel, ggsci, psych, tibble, rlang, SingleCellExperiment
Suggests: knitr, rmarkdown
Published: 2022-09-26
Author: Yifan Zhang [aut, cre], Duc Tran [aut], Tin Nguyen [fnd], Sergiu M. Dascalu [fnd], Frederick C. Harris, Jr. [fnd]
Maintainer: Yifan Zhang <yfzhang at>
License: LGPL-2 | LGPL-2.1 | LGPL-3 [expanded from: LGPL]
NeedsCompilation: no
CRAN checks: scTEP results


Reference manual: scTEP.pdf
Vignettes: scTEP


Package source: scTEP_0.1.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): scTEP_0.1.0.tgz, r-oldrel (arm64): scTEP_0.1.0.tgz, r-release (x86_64): scTEP_0.1.0.tgz, r-oldrel (x86_64): scTEP_0.1.0.tgz


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