Bioconductor Spatiallibd

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spatialLIBD

updated 9 months ago by Leonardo Collado Torres ★ 1.1k • written 9 months ago by Oliver • 0

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spatialLIBD

updated 3.1 years ago by Leonardo Collado Torres ★ 1.1k • written 3.1 years ago by kstern • 0

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spatialLIBD

updated 3.1 years ago by Leonardo Collado Torres ★ 1.1k • written 3.1 years ago by kstern • 0

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spatialLIBD

updated 3.6 years ago by Leonardo Collado Torres ★ 1.1k • written 3.7 years ago by Ma • 0

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spatialLIBD

updated 4.1 years ago by Leonardo Collado Torres ★ 1.1k • written 4.2 years ago by Dimitri • 0

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biorxiv spatialLIBD News

written 5.6 years ago by Leonardo Collado Torres ★ 1.1k

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Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0

Exactly, MDS was computed on logCPM values from `cpm(x, log=TRUE)` after running `calcNormFactors(method="TMMwsp")` on the DGE object. I al…

Answer: GO.db and others package Download failure by James W. MacDonald 68k

You didn't get an error. You didn't even get a warning! You simply got a message saying that two (unrelated) packages were not updated. As …

Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k

MDS of what quantity? LogCPM from `cpm()`? I don't have a definitive answer, but my feeling that is that library size effects are to be ex…

Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0

Apologies for not clarifying earlier, you're right: it is a PCA, not an MDS. In local machine, computing the MDS takes quite a long time, P…

Answer: replace cat with message in glmTreat when lfc = 0 by Gordon Smyth 53k

Yes, I agree that the message should be a `message` rather than `cat` output, and the message is perhaps not needed at all, because anyone …