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Comment: Mostly increased counts in differentially accessible peaks using DESeq2
by
Ricardo Iván
• 0
Hi Michael, Thanks for your reply. After reviewing the PCAs, maybe the issue that despite the replicates looking similar, there is still a…
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 …
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Answer: When running contrasts, does it use normalized read counts?
Comment: featureCounts fails to load annotation file
Answer: How to reverse complement some elements of a DNAStringSet
Answer: KEGGgraph result difference
Answer: What should be the normalization protocol for RNA seq data for WGCNA?
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