SCORPIUS: Inferring Developmental Chronologies from Single-Cell RNA Sequencing Data

An accurate and easy tool for performing linear trajectory inference on single cells using single-cell RNA sequencing data. In addition, 'SCORPIUS' provides functions for discovering the most important genes with respect to the reconstructed trajectory, as well as nice visualisation tools. Cannoodt et al. (2016) <doi:10.1101/079509>.

Version: 1.0.9
Depends: R (≥ 3.5.0)
Imports: dplyr, dynutils (≥ 1.0.3), dynwrap, grDevices, ggplot2 (≥ 2.0), lmds, MASS, Matrix, mclust, methods, pbapply, pheatmap, princurve (≥ 2.1.4), purrr, ranger, RANN, RColorBrewer, reshape2, stats, tidyr, TSP
Suggests: anndata, covr, knitr, reticulate, rmarkdown, Seurat, SingleCellExperiment, testthat (≥ 2.1.0)
Published: 2023-08-07
DOI: NA
Author: Robrecht Cannoodt ORCID iD [aut, cre] (rcannood), Wouter Saelens ORCID iD [ctb] (zouter)
Maintainer: Robrecht Cannoodt <rcannood at gmail.com>
BugReports: https://github.com/rcannood/SCORPIUS/issues
License: GPL-3
URL: https://github.com/rcannood/SCORPIUS, http://rcannood.github.io/SCORPIUS/
NeedsCompilation: no
Citation: SCORPIUS citation info
Materials: README NEWS
In views: Omics
CRAN checks: SCORPIUS results

Documentation:

Reference manual: SCORPIUS.pdf
Vignettes: Running SCORPIUS on a AnnData object
Investigating dendritic cell maturation in dendritic cell progenitors
Trajectory inference from simulated data
Running SCORPIUS on a SingleCellExperiment object

Downloads:

Package source: SCORPIUS_1.0.9.tar.gz
Windows binaries: r-devel: SCORPIUS_1.0.9.zip, r-release: SCORPIUS_1.0.9.zip, r-oldrel: SCORPIUS_1.0.9.zip
macOS binaries: r-release (arm64): SCORPIUS_1.0.9.tgz, r-oldrel (arm64): SCORPIUS_1.0.9.tgz, r-release (x86_64): SCORPIUS_1.0.9.tgz, r-oldrel (x86_64): SCORPIUS_1.0.9.tgz
Old sources: SCORPIUS archive

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