Man pages for HectorRDB/condimentsPaper
Package to accompany the condiments Paper
| 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... |
| anayze_multiple_conditions | Analyse dataset with three conditions |
| clean_results | Clean the output from the various simulation |
| complex | Results on the one bifurcation and three conditions datasets |
| complex_sce | A SingleCellExperiment example of a one bifurcation and three... |
| condRes_monocle | A data.frame object |
| create_5_lineages_simu | Create a bifurcating trajectory with five lineages and three... |
| 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 |
| fibrosis | A SingleCellExperiment object |
| five_lins | Results on the five lineages datasets |
| fivelin_sce | A SingleCellExperiment example of 5 lineages and two... |
| fork | Results on the one bifurcation and two conditions datasets |
| fork_sce | A SingleCellExperiment example of a one bifurcation and two... |
| 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.. |
| kras | A SingleCellExperiment object |
| pipe | Pipe operator |
| 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 |
| step1_fail | Results of the unstability test |
| tcdd | A SingleCellExperiment object |
| tgfb | A SingleCellExperiment object |
| tree | Results on the two bifurcations and two conditions datasets |
| tree_sce | A SingleCellExperiment example of a two bifurcations and two... |
| unstability | Results of the unstability test |
