jfouyang
commented
3 years ago Hi, there are currently no plans to include functionality to plot scATAC-seq peaks in the short term, although I imagine that it will be really useful with increasing usage of single-cell multi-omics e.g. the 10X kits.
The main reason for that is that I personally do not have much experience in analyzing scATAC-seq data. Thus, it would be difficult for me to identify what visualizations would be useful to fellow computational people as well as wetlab co-workers. Furthermore, peak-based visualizations are generally more computationally intensive and take up more memory (both RAM and disk wise) since the bed / big wig files have to be stored and queried. That would require quite a fair bit of optimization to create a seamless web interface.
That said, in principle, ShinyCell would be able to display single-cell multi-omics data if they are count-based. Thus it would be possible to make a tab containing gene expression (GEX) data and another tab containing ATAC counts. Or you can merge the GEX and ATAC assays, allowing you to visualize them both simultaneously. Note that this can apply to Antibody-derived tags from CITE-seq experiments as well.
Would this "hack" work for you?
Hello First of all : Congratulation for your tool ! We are using it a lot in our laboratory. It is the best tool to quickly put our single cell experiment on our Rserver so it can be analysis by the biologists.
I was wandering if you had plan to put capability for Cellranger multiome experiments ? I already did something in R markdown where I can display scATACSeq feature plot of peaks + scRNASeq feature plot of corresponding genes. It helps decipher if accessibility is link to gene expression for gene cell markers.