dyngen
dyngen copied to clipboard
dynverse
Simulating single-cell data using gene regulatory networks 📠
According to the vignette, this is the way to create a knockdown simulation: 0 ```r b3_genes % filter(module_id == "B3") %>% pull(feature_id) model_ko
How can we elucidate the ground truth for the mol_mrna from the dyngen object? I am following the tutorial [here]( https://dyngen.dynverse.org/articles/getting_started.html#step-5-simulate-gold-standard). Following code prints out the expression trends for the...
Hi, Thank you for amazing works. I'm encountering an issue while attempting to generate a knockdown model and would appreciate some help. I have successfully followed the [tutorial](https://dyngen.dynverse.org/articles/advanced_topics/simulating_knockouts.html) to generate...
I am opening this issue as a notification because `dyngen` is listed [here](https://cran.r-project.org/web/packages/Seurat/index.html) as a package that relies (depends/imports/suggests) on Seurat. As you may know, we recently released Seurat v5...
Hi, I noticed that in one generated dataset there is only one trajectory. If I simulated two datasets with 2 kinds of trajectories, can I combine them together in one...
Hi, When I am simulating the batch effect, I am wondering if there exists any parameters or functions that can adjust the batch effect strength in the simulated dataset. Looking...
I receive the following ```R Error in `vectbl_as_row_location()`: ! Must subset rows with a valid subscript vector. ✖ Subscript `best_match` has the wrong type `list`. ℹ It must be logical,...
Why do I get this error message when running generate_gold_standart?
Thank you for developing a great simulator! Is it possible to simulate expression changes after knocking out multiple genes simultaneously (e.g. double knockouts, triple knockouts, etc.) using simulation_type_knockdown()? Thanks!
Dear All, I finally managed to install dyngen and Rstudio is not crashing anymore. However when I try so generte datasets it gives me the following errors (doesn't stop though)...