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Recent Replies
Answer: Get relationships and hierarchies for GO terms
by
rfran010
▴
130
Maybe stringdb? seems to have an option to do what you describe.
https://string-db.org/cgi/input?sessionId=bmYwdg48WePq&input_page_activ…
Comment: How to calculate TPM from featureCounts output
by
rfran010
▴
130
This file is your counts file, isn't it?
Comment: Help with running ATAC using Encode pipeline
by
rfran010
▴
130
Curious, can you give specific examples of what you refer to as "input file" and "json file"?
In the screenshot you shared, input files re…
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
by
rfran010
▴
130
What version are you running? I use v2.0.3 on the command line.
It looks like this option may be added in a later version, with `GTF.attrT…
Answer: Get relationships and hierarchies for GO terms
by
Vincent Laufer
★
2.9k
Hey Daniel,
**First, one potential caveat.**
Above, you say "I have obtained several GO terms (indicating function and biological proc…
Comment: Perl. How to retrieve data until a keyword in GenBank?
by
Fungi-Beware!
▴
10
THANK YOU!! Your method works!!
And by removing:
$data = '';
I figured out how to retrieve the annotation info with a prompt:
…
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
by
Yeeshouw
•
0
Yes, I am inputting a GTF file. I reviewed the `[featureCounts][1]` documentation, and I could not find this `extraAttributes` parameter. …
Comment: Italicise annotations with pheatmap
by
jamie.pike
▴
80
@ATpoint Very true! I'm not so familiar with many image editing software and I wonder if it will be just as quick for me to try in R, but I…
Comment: Italicise annotations with pheatmap
by
jamie.pike
▴
80
You're right, I was trying to save time and not write for in ComplexHeatmap, but using @Trivas ComplexHeatmap::pheatmap() should help! Than…
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
by
Yeeshouw
•
0
Thank you very much for information! I am able to see this column you mention.
Comment: Italicise annotations with pheatmap
by
ATpoint
72k
I might be the party pooper but I generally think that these sorts of aesthetics should be done later in something like Inkscape. In R do t…
Comment: Embryo transcriptome
by
ATpoint
72k
Just one, that is how the convention is. One sample (SRX...) can have one or many SRR entries. If many you can merge them prior to quantifi…
Comment: What kind of statistical test does Cellranger count use?
by
ATpoint
72k
Clustering is not a statistical test with p-values. It is unclear what you mean. Actually, I would just ignore everything that the blackbox…
Comment: Information on sequin RNA spike in standards
by
Ram
39k
I'd try emailing the authors for a link.
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