SCORPIUS-package: SCORPIUS: Trajectory inference from single-cell RNA...

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

Description

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).

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
)

SCORPIUS documentation built on July 1, 2020, 5:38 p.m.