From f444467585b377fcff2873dfc994f86cdcc5ff58 Mon Sep 17 00:00:00 2001 From: r-trimbour Date: Wed, 10 Apr 2024 14:22:11 +0200 Subject: [PATCH] update GRNBoost2 recommendation --- vignettes/chen_vignette.Rmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) 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`).