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Recent Replies
Comment: Perfom a Gene Ontology Analysis from GO terms txt file
by
sansan_96
▴
80
Your table should look like this (GO terms):
```
geneid GOid
Zm00001eb000010 GO:0003690;GO:0003727;GO:0019843;GO:0005739
Zm00001eb000020 G…
Answer: Perfom a Gene Ontology Analysis from GO terms txt file
by
sansan_96
▴
80
I understand, here is an example with topGO where you need a differential expression table (DESeq2 for example) and a table of GO terms:
`…
Comment: Perfom a Gene Ontology Analysis from GO terms file
by
Hamtaro
▴
50
Thank u for your reply. The problem is that I used the genome and gene annotation from that webpage, not ensemble or ncbi, so I have to use…
Comment: Perfom a Gene Ontology Analysis from GO terms file
by
sansan_96
▴
80
Hello,
To perform functional enrichment analysis there are packages such as topGO or clusterProfiler that can work very well. Lately I've …
Answer: Post-imputation plot
by
LChart
3.9k
The anti-diagonal band does suggest some fraction of genotypes are strand-flipped - probably G/C or A/T variants.
Comment: Differential Accessibility
by
Ram
43k
Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the cod…
Comment: Extract protein sequence
by
anna
▴
20
Thank you! I need this for eukaryotic organism and known protein sequences, but I guess seqkit would work well!
Comment: Landmark gene selection in L1000.
by
GenoMax
141k
Paper referred to in question: https://pubmed.ncbi.nlm.nih.gov/29195078/
> so I want to understand how you reduced the 12063 genes to 978…
Comment: Batch effects : ComBat or removebatcheffects (limma package) ?
by
cwwong13
▴
40
@kevin May I know whether your comments and edits were mainly based on the fact that "Previously, [crazy] people had been using the origina…
Comment: Programmatically retrieving positions of protein active site residues
by
Wayne
★
2.0k
Wow, I was shocked at this AI answer that looks to be a good start for using UniProt. Sharing it in case it is useful. (It will work in ses…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴
570
> Can you clarify what you mean by "100% of reads pass cutadapt, even
> though 70% of reads contain adapters and get trimmed.
The header o…
Comment: Software to separate reads from different individuals
by
GenoMax
141k
If you have independent information available (e.g. genotype data for both individuals) then you *may* be able to assign reads based on the…
Answer: Extract protein sequence
by
Matthias Zepper
4.5k
You didn't mention what kind of organism you are working with and what kind of protein you are looking for?
If it happens to be a microbia…
Comment: How to use limma to find differentially expressed genes in response to a continu
by
pairedttest
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10
Thank you Gordon for your expertise. One question that I have now that I have a list of DE genes is how to interpret logFC of this continuo…
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