Lucy Garner
Lucy Garner
Hi, I was wondering whether you have compared the success of pySCENIC analysis at identifying "true" gene modules downstream of different normalisation methods. In particular, I am interested in whether...
**Describe the bug** Error when running pyscenic grn. I am using an older version of dask (1.0.0) as previously suggested. **Steps to reproduce the behavior** 1. Command run when the...
**Describe the bug** This may be a bug or a user-error, but I am unable to use custom thresholds in the binarize function **Steps to reproduce the behavior** 1. Command...
** If this is a question and not a bug report or enhancement request, please post to our google group at https://groups.google.com/forum/#!forum/monocle-3-users** **Describe the bug** Error in plot_cells in that...
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, I was wondering whether RNA velocity works well for 5' 10x data and if the results are similar to 3' data? Many thanks, Lucy
Hi, I just upgraded my R version from 4.0.0 to 4.0.1. It was working perfectly fine on 4.0.0 before. I was wondering why in my RSwitch menu, it now says...
Hi, Thank you for generating this great function. I would like to be able to generate a correlation plot that is coloured by the correlation values, but the squares (or...
Hi, I would like some advice on the appropriate batch variable for my experimental design. I have samples from 8 different individuals - for 3 of these, I have cells...