Hurley

Specific types of BND

2

Hi, could you please provide a script for converting BND svtype to specific SV types, e.g. DEL, DUP. I don't think the one in #4 is accurate. Thanks,

data leakage problem in your model

1

The design of your adjacency matrix `adj_mats_orig` and the way you split the train/test set will cause a huge **data leakage problem** in your training, because your validation and test...

Hi, I would like to try to use your model to prioritize genes associated with diseases that are not included in your training dataset. I have phenotype data and I...

Why do you only train the model for 1 epoch?

2

Hello, Nice work! Just wondering is there any specific reason why you only trained the model for one epoch? Thanks! Hurley

cannot install r-scgnnltmg

2

Hi, I tried to install r-scgnnltmg `conda install -c cyz931123 r-scgnnltmg`, but it says ``` ackagesNotFoundError: The following packages are not available from current channels: - r-scgnnltmg ``` Could you...

why so many "outliers" when focusing on a specific cell type?

8

Hi, It seems that when I run Metacells focusing on a particular cell type (e.g. myeloid cell only, or T cell only), the program will call out many outliers with...

Hi, Thanks for posting these fantastic material from last year! I'm wondering if you are planning a scWorkshop this year. Thanks Hurley

how to interpret output file

1

Hi, I've successfully run the VVP and got the output result (Hooray!), just wondered how should I interpret the output file, and what does each column mean in the output?...