jsb-ucla / scdesign2 Goto Github PK

Hello,

Thank you for creating this simulator software that can address multiple issues. I am currently working on a pipeline that I need to validate using simulated reads. I had a few questions about this software:

1. Will scDesign2 be able to produce raw reads from 10X? I will require raw reads and not just read counts.
2. Is it possible to provide mutated genes to scDesign2 and have it produce reads from that and not the WT version?
3. scDesign2 is designed to capture gene correlations from the underlying data and then simulate reads. Will it be possible to skip this step and have reads produced from the genes directly? For our purpose, we do not require to capture or model gene correlations.

Thank you.

Hi,

While running scDesign2 I received the following error:

The actual counts I used as input to scDesign2 were obtained from the Mouse Olfactory Bulb dataset from the following:
https://www.spatialresearch.org/resources-published-datasets/doi-10-1126science-aaf2403/

I was wondering if there is a way to resolve this issue?

Hello JSB-UCLA,

I have a question for you. I was looking for synthetic scRNA seq data that would resemble my own scRNA seq data sets and which I could use to test the performance of two methods of differential gene expression. I was wondering if synthetic data generated by scDesign2 can be used for this particular purpose. More specifically, I wanna compare the two methods in terms of their type I and type II error rates using a synthetic data set in which the ground truth is known.

You mentioned in your paper that:

• ScDesign2 should retain every gene’s distribution of expression levels in its synthetic data without deleting genes in real data. This property is essential for benchmarking differential gene expression analysis.

• scDesign2 can assist differential gene expression analysis. Its estimated marginal distributions of individual genes in different cell types can be used to investigate more general patterns of differential expression (such as different variances and different zero proportions), in addition to comparing gene expression means between two groups of cells.

However, I am not sure how one can perform this benchmarking practically using the package. I checked the vignette and could not find relevant information about this particular application.

If you could kindly elaborate more on how I can perform this comparison using scDesign2, I would be really grateful !

Thank you very much for your time and help.

Best regards,
Ismail