Tinyi Chu

Hi. Sorry for the delay. Could you please include the exact function call and the error reported? Thanks. On Wed, Nov 8, 2023 at 2:07 AM faenee ***@***.***> wrote: >...

Hi Almog, Thank you for your interest in our method. Yes. You can perform DE analysis by comparing each cell type vs every other cell type, and then select the...

Hi. Thank you for your interest in our work. Although BayesPrism is robust to biological variation in the context of tumor heterogeneity, it is hard to predict the extent to...

Thank you for your interest in our methods. Please refer to the vignette and use the rdata from tutorial.dat as an example. Thanks. On Thu, Dec 14, 2023 at 11:34 ...

Hi. Cell state is used to model cell types with gene expression following a continuum, where a confident clustering is difficult to achieve, whereas cell type is for discretized clusters....

Dear user, Thank you for your interest in our methods. One possibility could be that no genes showed significant differential expression for stromal cells, which can be caused by 1)...

Dear user, Thank you for reporting this issue. We have fixed it. Please try re-submitting your task. Best, Tinyi On Sat, Dec 16, 2023 at 10:48 AM soph1azhao ***@***.***> wrote:...

Hi William, Thank you for your interest in our method. We do not have a docker image yet, as the installation of BayesPrism is relatively straightforward. We are certainly open...

Hi William, Sorry for the late reply. I am not entirely sure, but it could be caused by a version issue of scran. I tested 4.2.1 and 4.1.3, and it...

Hi Vish, I believe vst transformation internally accounts for library size. You may see this for details: https://rdrr.io/bioc/DESeq2/man/varianceStabilizingTransformation.html . But you may certainly use log2 (library size normalized count +...