Man pages for SGDDNB/GeneSwitches
Discover the order of gene regulatory events during cell state transitions
| binarize_exp | Binarize gene expression |
| common_genes | Identify common switching genes between paths |
| common_genes_plot | Plot common switching genes between paths |
| convert_monocle2 | Convert monocle2 output into GeneSwitches object |
| convert_slingshot | Convert slingshot output into GeneSwitches object |
| distinct_genes | Identify distinct switching genes for each path |
| downsample_zeros | Random downsampling of zero expression |
| filter_switchgenes | Extract switching gene list of interesting |
| find_switch_logistic_fastglm | Fit fast logistic regression and find switching timepoint |
| find_switch_pathway | Find significantly changed pathways and switching timepoint |
| get_example_inputData | Download example input data |
| gs_genelists | An example of gene lists |
| merge_pathways | Merge redundant pathways |
| msigdb_h_c2_c5 | An example of gene sets |
| phyper_pathway | Find significantly changed pathways and switching timepoint |
| plot_gene_exp | Plot gene expression |
| plot_monocle_State | plot monocle2 trajectory colored by State |
| plot_pathway_density | Pathways ridge plot |
| plot_timeline_ggplot | Plot switching genes |
| reduce_pathways | Reduce redundant pathways |
| subset_pseudotime | Subset GeneSwitches object based on the range of pseudotime |
