Di Wu

Not all clusters were annotated when "per-cluster" method was used

1

Thanks for developing this wonderful tool for scRNASeq! I've been using "per-cell" method to annotate my data, it worked very well. Recently, I started to use "per-cluster" method to annotate...

Request dot scale parameter for Clustered_DotPlot

3

Thank you for developing this package to make my life easier! I was wondering if a dot scale parameter can be added to Clustered_DotPlot function. In DotPlot_scCustom function, which is...

Thanks for developing the tool! After running the superreads.pl, the LongReads.fq file is empty. But in work1 directory, the superReadSequences.fasta file looks like some assembled superreads. I wonder what the...

UMAP looks like a line when neighborhood size was determined by using cell type labels

5

Thanks for the useful tool! I noticed that in my results, some areas look like solid lines (for example the cluster at the top in the screenshot below) in the...

Integrating Ambient RNA Removal (CellBender) into Velocity Analysis

1

Thank you for developing such a valuable tool—our velocity-related analyses heavily depend on it. We recently started incorporating ambient RNA removal (e.g., using [CellBender](https://github.com/broadinstitute/CellBender)) into our scRNA-seq analysis pipeline. However,...

Recommendation of method for inferring gene expression trends along latent time

1

Hi VeloVAE team, Thanks for developing this tool, it is my favorite RNA velocity analysis tool so far! I wanted to infer and plot a trend line for gene expression...