sctransform
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satijalab
R package for modeling single cell UMI expression data using regularized negative binomial regression
Hi Christoph, I am running SCTransform with batch_var and encounter this error: "Error in while ((it eps) { : missing value where TRUE/FALSE needed". Here is the full error: >...
Hi Christoph, Loading the Rfast package triggers a Node Stack Overflow Error in SCTransform. The error message is the same as the one seen e.g. here (https://github.com/satijalab/seurat/issues/3904) and here (https://github.com/ChristophH/sctransform/issues/87)....
Hi Christoph, absolutely phenomenal tool set, I'm really excited by the possibility to run DE testing on the output of sctransform! I was wondering if you could comment on what...
Velocyto
Can scTransform be used to normalize the output .loom files from running Velocyto to assess RNA velocity?
I'm trying to load multiple scRNA datasets, merge them, and run SCTransform, but I'm getting the following error: ``` warning: solve(): system seems singular; attempting approx solution Error in qpois_reg(regressor_data,...
Hi, I was wondering whether the sctransform normalisation is able to account for changes in RNA composition between conditions. I have a dataset of non-activated and TCR-activated T cells. I...
Hi, I would like to use pySCENIC (https://www.nature.com/articles/s41596-020-0336-2) to identify modules of genes predicted to be regulated by a given transcription factor (regulons). I was wondering whether scRNA-seq data that...
Hi Christoph, Thank you for the great work of SCTransform! Not only is the paper well-written, but also the implementation is brilliant. I just have one confusion after reading the...
Hi Christoph, I was hoping you could provide more details on how the batch_var option works. In the paper you state "we first learn regularized models using only the sequencing...
Hi Christoph, Thanks for all your work. When we use Scaledata we can specify the gene, for example"pbmc
