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Comment: WGCNA with TPM tables
by
ATpoint
★
4.5k
WGCNA is not a Bioconductor package, but generally:
If you want to do serious analysis then find the raw data. There is no guarantee what …
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
by
Paul
•
0
You are an absolute lifesaver, thank you so much for the clarification!
Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
by
James W. MacDonald
67k
The `EnsDb.Mmusculus.v79` package is mm38, not mm39. If you want a current `EnsDb`, use `AnnotationHub`
```
> library(AnnotationHub)
>…
Comment: Identical samples after deseq2 batch effect removal
by
Michael Love
42k
I'm adding my comment to the threaded section ...
I don't have any suggestions here but whatever method you're using is not appropriate up…
Comment: ANOVA like approach of edgeR
by
Yunshun Chen
▴
880
If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …
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