muscat
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HelenaLC
Multi-sample multi-group scRNA-seq analysis tools
Hello everyone, I am using the Muscat Pipeline following the tutorial found on Bioconductor. I start from a Seurat Object that I convert into an SCE object and run the...
The muscat bioconductor page says that  Where $\lambda_c$ is a cell dependent parameter. Now for each cell that we simulate the sim_mean for a...
Hello, This is directly related to [issue 119](https://github.com/HelenaLC/muscat/issues/119). We evaluated muscat's implementation of limma-voom. It seems it ignores the observation weights from voom and solely uses weights for each sample...
In [`muscat:::.limma`](https://github.com/HelenaLC/muscat/blob/master/R/utils-pbDS.R#L104), the call to `limma::lmFit` passes `weights = w`. I believe this tells limma to completely ignore the voom weights stored in `y` and use `w` instead. I'm guessing...
Dear MUSCAT team, First of all, thanks for creating this great package. I was wondering how the AveExpr in the output of mmDS is calculated? And how can I calculate...
Hi, can you please let me know if my understanding is correct in this issue. Thank you!!! https://github.com/HelenaLC/muscat/issues/102#issue-1203975480
Hi, In resDS function - you calculate cpm from y$data[[k]] .This will work for edgeR as this returns normalized count but will not work when using limma-voom. - as.matrix(y$data[[k]]) returns...
Hi, Thanks for creating and maintaining muscat, and all your hard work that goes into method development and benchmarking! I think there is a bug/inconsistency in the sign of the...
Hi @CATALYST-project, Thanks for maintaining this super useful package. I made a small change to the `pbDS` function so that the parameters used by `edgeR::filterByExpr` and `nmads` are modifiable by...
Added through the `positive_type` argument to force the type genes to be positively/ negatively/ randomly differential compared to the other clusters.
