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Answer: SingleR with multiple single cell references
by
Aaron Lun
★
28k
> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…
Answer: Automatically install dependencies
by
ATpoint
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4.7k
The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…
Answer: To count or not to count multi-overlapping reads?
by
Gordon Smyth
52k
> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand?
Overlapp…
Comment: Weird p-values using DESeq2?
by
ATpoint
★
4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2?
by
Wolfgang Huber
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13k
Dear Ingrid,
thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
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