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Gordon Smyth
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Popular Question to
Payal
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Rory Stark
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v.berriosfarias
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Recent Replies
Comment: Limma returned only positive logFC values
by
Gordon Smyth
★
6.1k
No, the updated code is no more correct than your original code.
Before you undertake any differential expression analysis, you need to ha…
Answer: Adjusting for batch effect and covariates with ComBat
by
zahra.elahi
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0
For your first question that is "Shouldn't PCA analysis of combat_tpm look more homogenous than the original dataset?", NO, because you inc…
Answer: plyranges:: summarise() not recognizing previous summarized column (counts)
by
Alewa
▴
120
solved, thanks!
```
#calculate the proportions of cpgs per chrom
counts_cpgr <- cpgr %>% group_by(seqnames) %>% summarise(cnts = n())
count…
Comment: Limma returned only positive logFC values
by
melissachua90
▴
40
Thank you for your comments. I've updated my code:
group <- factor(type, levels=c("1a", "1b", "1c", "2a", "2b", "2c"))
design <- m…
Comment: Creating a local version of Clustered NR database
by
GenoMax
130k
> One idea is to provide just the representative sequences as a first
> pass.
This seems reasonable since it should capture significant pa…
Comment: pal2nal -nogap -nomismatch options not working
by
Marie
•
0
Hi, did you end up solving this? I am running into the same issue.
Marie
Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴
130
and what about enhancer? is it possible to do it from a bulk-RNAseq?
Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
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130
yes! clearly the terminology on my side needs to improved!
Comment: How to get information about promoter from bulk-RNAseq?
by
rpolicastro
12k
Generally speaking, most promoters only initiate transcription for a single gene, with a single gene potentially having multiple promoters …
Answer: How to get information about promoter from bulk-RNAseq?
by
Trivas
★
1.2k
I'd probably select the genes of interest from your bulk RNA-seq results then use the UCSC table browser to get the sequence upstream of th…
Comment: How to add annotation columns with specific colors to the heatmap?
by
Ram
39k
Show us your exact code - it is quite easy to tweak colors in ComplexHeatmap with the `col=` argument.
Comment: VCF file CSQ flag
by
Ram
39k
True, but it's not technically impossible to annotate GVCFs, which is why I did not address that point.
Comment: Creating a local version of Clustered NR database
by
PeterC_NCBI
▴
260
@genomax Sorry for the delay in reply. We're still working out the details of what exactly to provide. One idea is to provide just the rep…
Comment: Shannon's Entropy by Sliding Window in R
by
rohitsatyam102
▴
690
Hi
Were u able to achieve this?
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