What are still some missing tools for RNA-seq or single-cell RNA-seq data that exist for microarray data ?

Question

[K. Bedejova]

Hello! I'm doing an extensive research on bioinformatics tools for RNA-seq and microarray data. Microarrays have been around longer than RNA-seq and one thing that particularly interests me is if there are any tools that are available and frequently used for microarray data but are still missing for RNA-seq data.My second question is, are there perhaps any tools that are being used for RNA-seq data but have not been implemented for use on single-cell RNA-seq data ?

Thanks a lot in advance.

Answer 1

[Devon Ryan]

The only tool group that I know of that exists for microarrays but not RNAseq is for signal source separation (ICA, etc.). There are tools that state that they can do this for both, but I've never found them very believable. I should note that this lack of believable tools is due to the nature of RNAseq, so you can't just take a microarray method and rewrite it for RNAseq, you need a completely different mathematical method that may well be impossible (i.e., due to the innate information loss from multiple signals mixing in a competitive 0-sum manner).