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SCORPIUS: Trajectory inference from single-cell RNA sequencing data.

Source: R/package.R
SCORPIUS-package.Rd

SCORPIUS orders single cells with regard to an implicit timeline, such as cellular development or progression over time.

Dimensionality Reduction functions

reduce_dimensionality

Trajectory Inference functions

infer_trajectory, infer_initial_trajectory, reverse_trajectory, gene_importances, extract_modules

Visualisation functions

draw_trajectory_plot, draw_trajectory_heatmap

Datasets

generate_dataset, ginhoux

References

Cannoodt R. et al., SCORPIUS improves trajectory inference and identifies novel modules in dendritic cell development, bioRxiv (Oct., 2016). doi:10.1101/079509 (PDF).

See also

Useful links:

Author

Maintainer: Robrecht Cannoodt rcannood@gmail.com (ORCID)

Other contributors:

Examples

## Load dataset from Schlitzer et al., 2015
data("ginhoux")

## Reduce dimensionality and infer trajectory with SCORPIUS
space <- reduce_dimensionality(ginhoux$expression, "spearman")
traj <- infer_trajectory(space)

## Visualise
draw_trajectory_plot(
  space,
  path = traj$path,
  progression_group = ginhoux$sample_info$group_name
)
#> Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
#> ℹ Please use tidy evaluation idioms with `aes()`.
#> ℹ See also `vignette("ggplot2-in-packages")` for more information.
#> ℹ The deprecated feature was likely used in the SCORPIUS package.
#>   Please report the issue at <https://github.com/rcannood/SCORPIUS/issues>.
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the SCORPIUS package.
#>   Please report the issue at <https://github.com/rcannood/SCORPIUS/issues>.
#> Ignoring unknown labels:
#> • fill : "Group"