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Recent Replies
Comment: Get relationships and hierarchies for GO terms
by
Alexander
▴
70
For R-users might be interesting to look at notebook "CAFA5: train set GO terms" https://www.kaggle.com/code/antoninadolgorukova/cafa5-trai…
Comment: Getting Pairwise Sequence Alignment Score With Biopython
by
Alexander
▴
70
Thanks for sharing ! Just these days I am trying to wrap my mind on protein alignments.
I wonder: 1) "PID" in your post is "percentage o…
Answer: What kind of statistical test does Cellranger count use?
by
fracarb8
▴
950
You should read the [cellranger documentation][1] to understand how the analysis are performed. For example, it uses `graphclust` for clust…
Answer: Gene prediction software
by
alexandru.bologa.marian
▴
40
Hi,
I don't know if there are tools designed to predict pseudogenes, but If i understand correctly from your post you could predict all th…
Answer: Getting Pairwise Sequence Alignment Score With Biopython
by
Jonathan Lefebre
▴
60
Maybe quite late, but in case other people are looking for this. Pairwise sequence identity can be easily calculated using basic python fun…
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…
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