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Comment: Using Normalized Counts in DESeq2
by
Michael Love
42k
Also, just to add, there are many dozens of posts on this topic of DESeq2 applied to TCGA counts, normalized or other. Recommend google sea…
Answer: Using Normalized Counts in DESeq2
by
ATpoint
★
4.5k
TCGA raw counts can be obtained for example using the TCGAbiolinks or recount packages.
Comment: How to reverse complement some elements of a DNAStringSet
by
Christine Jones
•
0
Fantastic, thank you
Comment: When running contrasts, does it use normalized read counts?
by
Katherine
•
0
Ok, so the comment I was given where they said DeSeq2 should be with normalized counts is incorrect.
the ```normalized_counts``` variable …
Answer: How to reverse complement some elements of a DNAStringSet
by
James W. MacDonald
67k
You should always try the vectorized method first, rather than looping.
```
> myFasta[myFasta_rc] <- reverseComplement(myFasta[myFasta_…
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