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Thank you for developing Bulk2space, it is a very exciting tool and I had the chance to work with it for a while now.
I have few questions about its usage:
Is bulk2space suitable to compare single cells datasets generate from two different bulk RNA-Seq datasets? For example, let's say I have bulk RNA-Seq datasets from a control and a treatment group. Can I feed these into bulk2space with the aim to compare how the expression in single cells changes between the two groups? If so, should you use the same references when deconvoluting and only change the bulk datasets?
Can bulk2space be used to identify potentially new cell types OR new subpopulation within known cell types?
Lastly, can you use reference datasets from different species? For example, let's say I want to deconvolute a bulk human kidney; can I supply a mouse single cell dataset of kidney tissue and then a human spatial transcriptomics reference for the mapping step? The reason I ask this is because right now there are very limited reference datasets for my organism and organ of interest, so maybe using a similar species could be feasible?
I am looking forward to hearing from you, I hope you can advice on these scenarios.
Once again, many thanks for developing such an exciting tool. It will be of great use to the scientific community.
The text was updated successfully, but these errors were encountered:
AlexUOM
changed the title
Potential applciations of Bulk2Space
Potential applications of Bulk2space
Jul 17, 2023
Thank you for developing Bulk2space, it is a very exciting tool and I had the chance to work with it for a while now.
I have few questions about its usage:
Is bulk2space suitable to compare single cells datasets generate from two different bulk RNA-Seq datasets? For example, let's say I have bulk RNA-Seq datasets from a control and a treatment group. Can I feed these into bulk2space with the aim to compare how the expression in single cells changes between the two groups? If so, should you use the same references when deconvoluting and only change the bulk datasets?
Can bulk2space be used to identify potentially new cell types OR new subpopulation within known cell types?
Lastly, can you use reference datasets from different species? For example, let's say I want to deconvolute a bulk human kidney; can I supply a mouse single cell dataset of kidney tissue and then a human spatial transcriptomics reference for the mapping step? The reason I ask this is because right now there are very limited reference datasets for my organism and organ of interest, so maybe using a similar species could be feasible?
I am looking forward to hearing from you, I hope you can advice on these scenarios.
Once again, many thanks for developing such an exciting tool. It will be of great use to the scientific community.
The text was updated successfully, but these errors were encountered: