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Recent Replies
Comment: Getting same value for start and end position, "DNA methylation"
by
ATpoint
72k
Yes, that is what methylkit is for. See my answer.
Comment: Italicise annotations with pheatmap
by
ATpoint
72k
Inkscape you learn in a day, for basic image and figure manipulation it's really simple and a good skill to have. Highly recommended.
Comment: Installation of PPFinder
by
subashini.fbtpb106
•
0
Can you suggest me any software that does gene prediction by masking pseudogenes?
Comment: variant allelic fraction
by
Pierre Lindenbaum
154k
IMHO this is like asking for the cow when you only have a steak :-)
Comment: Getting same value for start and end position, "DNA methylation"
by
Pankaj
•
0
yes I am working on Bisulphate sequenced data.
Answer: Get relationships and hierarchies for GO terms
by
rfran010
▴
140
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
▴
140
This file is your counts file, isn't it?
Comment: Help with running ATAC using Encode pipeline
by
rfran010
▴
140
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
▴
140
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…
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