diff --git a/vignettes/chen_vignette.Rmd b/vignettes/chen_vignette.Rmd index 1feedfc..61376a8 100644 --- a/vignettes/chen_vignette.Rmd +++ b/vignettes/chen_vignette.Rmd @@ -195,9 +195,9 @@ hummus <- compute_tf_network(hummus, ### 2.4. Compute gene network from scRNA-seq w/ GENIE3 ### *!! This step can be very slow if you have thousands of cells !!* -#### Current recommendation if you have a big dataset is to compute the network -#### before with [GRNBoost2 thorugh arboreto](https://arboreto.readthedocs.io/en/latest/) -#### and [add it to the hummus object afterwards](https://cantinilab.github.io/HuMMuS/articles/add_networks.html). +_Current recommendation if you have a big dataset is to compute the network_ +_before with [GRNBoost2 thorugh arboreto](https://arboreto.readthedocs.io/en/latest/)_ +_and [add it to the hummus object afterwards](https://cantinilab.github.io/HuMMuS/articles/add_networks.html)._ Different methods can be used to compute the gene network. For now, only GENIE3 is implemented in HuMMuS. You can specify which assay to use to compute the network (`gene_assay`).