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 nevada.unr.edu> |
| License: |
LGPL-2 | LGPL-2.1 | LGPL-3 [expanded from: LGPL] |
| NeedsCompilation: |
no |
| CRAN checks: |
scTEP results |
Documentation:
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