Tinyi Chu

Hi Ying, Thank you for your interest in our methods. Please note that "MALAT1" is a human gene (an outlier gene in many human cancers). When using species="mm", try not...

Thank you for your interest in our methods. This shouldn't be a problem. Based on my experience, Visium data typically has fewer outliers than bulk RNA-seq.

Hi Roy, Sorry for the delay. The short answer is the final theta was designed to be at the target granularity. Cell states were used to model cells of similar...

Hi jh, Thank you for your question. The answer depends on the biological assumption about your data. For normal cells, since there is usually the corresponding cell state, for example...

Dear user, Thank you for your interest in BayesPrism. The short answer is that the entire scRNA-seq reference (gene-by-cell state matrix) and a single bulk data is sent to an...

Dear user, Thank you for your interest in our methods. We have not tested if microarray data can be used as reference. We noted one recent study that applied BayesPrism...

Hi Zhijie, Thank you for your questions. Please refer to this reply: https://github.com/Danko-Lab/BayesPrism/issues/56#issuecomment-1669620258 Best, Tinyi On Mon, Aug 19, 2024 at 12:54 AM ZhijieHanbioinfor ***@***.***> wrote: > Dear Dr. Chu, >...

Dear user, Thank you for your interest in our methods. It is always recommended to use the most comprehensive representation of cell types to build the scRNA-seq reference, as the...

Hi Rui-Jing, Sorry for the delay. Thank you for your feedback. I would be happy to help troubleshoot. Could you please provide additional details on how you specify the cell.type.labels...

Hi Yi-hua, Sorry for the delayed response. The memory usage depends on the #of cell types and cell states, #of bulk samples and #of genes. Below are a few suggestions...