Reference

Download the datasets for the case studies Those three functions obtain the dataset and metadata (mostly from GEO) and format them for analysis.
import_fibrosis()	Download and preprocess the raw dataset from .
import_KRAS()	Download and preprocess the raw dataset from Xue et al.
import_TCDD()	Download and import the raw dataset from Nault et al.
import_TGFB()	Download and import the raw dataset from McFaline et al..
Case study datasets The formatted datasets used in the simulations
condRes_monocle	A data.frame object
fibrosis	A SingleCellExperiment object
kras	A SingleCellExperiment object
tcdd	A SingleCellExperiment object
tgfb	A SingleCellExperiment object
Simulations All functions needed to run or analyze the simulations
all_metrics()	Compute all 5 metrics for a given FDR threshold
anayze_all()	Analyse dataset with two conditions
anayze_all_per_cond()	Analyse dataset with common and separate trajectories per condition
anayze_multiple_conditions()	Analyse dataset with three conditions
create_5_lineages_simu()	Create a bifurcating trajectory with five lineages and three conditions
create_bifurcating_simu()	Create a bifurcating trajectory with two conditions
create_bifurcating_three_conditions_simu()	Create a bifurcating trajectory with three conditions
create_consecutive_bifurcating_simu()	Create a trajectory with two bifurcations and two conditions
Visualization Functions to plot the results
plot_backbone_modulenet_simplify()	Plot simulation dataset by condition and cluster
plot_example()	Plot examples for figure 1
plot_reduced_dim()	Plot simulation dataset by condition and cluster
plot_reduced_dim_together()	Plot simulation dataset by condition
Simulation data The simulation results and examples
complex	Results on the one bifurcation and three conditions datasets
complex_sce	A SingleCellExperiment example of a one bifurcation and three conditions dataset
five_lins	Results on the five lineages datasets
fivelin_sce	A SingleCellExperiment example of 5 lineages and two conditions dataset
fork	Results on the one bifurcation and two conditions datasets
fork_sce	A SingleCellExperiment example of a one bifurcation and two conditions dataset
step1_fail	Results of the unstability test
tree	Results on the two bifurcations and two conditions datasets
tree_sce	A SingleCellExperiment example of a two bifurcations and two conditions dataset
unstability	Results of the unstability test