Sarah Bonnin

Hello, Thanks for this great package! I was wondering if there is a way to change the set names/labels ? My sets are originally called "3D: KO vs WT" and...

Hello, I am getting the following error with `music_prop.cluster`: ` Error in if (length(S) != ncol(D)) { : argument is of length zero ` I ran the function code line...

No such file or directory: '../data/GCN/training'

2

Hello, I installed the software and tried to run the toy example, but I get the following error: `No such file or directory: '../data/GCN/training'` There is no "GCN" in the...

How to create test_mask and train_mask?

1

Hello, It is not really an issue, but I wanted to ask advice on how to best create test_mask and train_mask vectors once you have the training and test datasets...

mm39 variants / black list

4

Hello, It is more a question than an issue: where would you look for a good resource of known variants for the mm39 assembly (and one for the "deny list")?...

Error: Attempting to add a different number of cells and/or features

2

Hi, I am running into the following error: ``` Error: Attempting to add a different number of cells and/or features ``` when trying to read in a .h5seurat file. I...

"Not enough valid cell type!" what is a good ct.sub parameter?

1

Hello, I was wondering how you decide for the "ct.sub" parameter, i.e. "subset of cell types that are selected to construct basis matrix" ? I get the "Not enough valid...

Cell type assignment in "coef"

2

Hello, I have a very basic question! After running the "init" and "optimize" steps, I obtain the coefficients with the deconvolve function: ``` ag.init(adata, celltype_key='Celltype') ag.optimize(ngen=5000, nfeatures=400, seed=0, mode="fixed") coef=ag.deconvolve(bulk_data,...