Tinyi Chu

Hi. BayesPrism reports the coefficient of variation for the posteriors theta0 and thetaf, but does not report this for Z, mainly due to consideration of computational and memory efficiency. On...

Not sure if I understand the question. For the exact math, please refer to the BayesPrism manuscript. For the code, please refer to the update_reference.R . On Thu, Dec 14,...

please refer to the vignette tutorial_deconvolution.html # extract coefficient of variation (CV) of cell type fractiontheta.cv wrote: > my question is if from Bayes Prism there is a way to...

Hi Wendy, Yes. BayesPrism works for both tumor and non-tumor datasets. Many of the benchmarks in our manuscript were done on non-tumor datasets, such PBMC and brain cells. Simply set...

Hi Seoyeon, Thank you for your interest in our methods. You may refer to our vignette and find examples in our tutorial data. Best, Tinyi On Fri, Jun 23, 2023...

Thank you for your interest in our methods. I would recommend direct run BayesPrism without performing batch effect correction on the bulk, as BayesPrism is highly robust to linear batch...

Hi The file `sc.dat` represents the scRNA-seq count matrix. Please note that the term "bulk" was a typographical error. I've corrected this in the updated vignette. Thank you for bringing...

only shared genes will be used for deconvolution. On Thu, Mar 7, 2024 at 10:11 AM Youcef BEN MOHAMMED < ***@***.***> wrote: > Hi The file sc.dat represents the scRNA-seq...

Hi Federico, Thank you for your interest in our methods. A simple answer to your question is you cannot use log-transformed / negative values in the corrected reference. It has...

yes. simply follow the vignette and set key=NULL in run.prism function. examples include the PBMC shown in the BayesPrism paper. On Wed, Dec 6, 2023 at 10:56 AM iwanttoeatyo ***@***.***>...