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Answer: DESeq2 interactions
by
prominentmirabel
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0
Good experimental setup! For HP vs CNP, try results(dds_int, contrast=list("pollutionpolluted", "temphot", "pollutionpolluted.temphot")). T…
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
by
ReinholdGaylord99
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0
Thank you so much!
https://www.nature.com/articles/s41467-021-25960-2
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
Gordon Smyth
53k
I'm not sure that I understand. You have a dataset that, even after pseudo-bulking, still has 6000 samples? That is surprising.
Retaining …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
abaed
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0
Hello again @gordonsmyth,
I've now applied the analysis using a more detailed annotation of cell types/clusters, which includes about 100 …
Answer: Sharing a collection of datasets in ExperimentHub
by
shepherl
4.2k
107 packages would be a lot! It is certainly possible (and recommended) to implement one package that utilizes ExperimentHub for controlli…
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