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17 results • Page 1 of 1

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Answer: DESeq2 interactions by prominentmirabel • 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 • 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 • 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…