Moderator: Jean-Karim Heriche
Jean-Karim Heriche ♦ 21k
- Reputation:
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- Location:
- EMBL Heidelberg, Germany
- Website:
- http://jkh1.github.io/
- Last seen:
- 33 minutes ago
- Joined:
- 8 years, 4 months ago
- Email:
- h******@embl.de
Posts by Jean-Karim Heriche
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... On the point of comparing some genes similarity with their GO similarity, you may be interested in [this paper][1] on which I collaborated.
[1]: http://europepmc.org/articles/PMC5304448 ...
written 8 hours ago by
Jean-Karim Heriche ♦ 21k
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... How do you go about the computation? Typical semantic similarity measures like Resnik's across GO biological process domain should take a few hours to compute for all ~20000 protein coding human genes without parallelization.
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written 8 hours ago by
Jean-Karim Heriche ♦ 21k
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... Do you need imputation to start with? For example, there are ways of doing PCA with missing values (e.g. this [paper][1]).
[1]: http://pbil.univ-lyon1.fr/members/dray/files/articles/dray2015a.pdf ...
written 1 day ago by
Jean-Karim Heriche ♦ 21k
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Comment:
C: Blast2Go Mapping Issues
... We don't do divination. You need to provide more info.
EDIT: More info means what software you're running, how, with what parameters, what kind of data you have ...
Do you have the right database set up? Are your blast parameters adequate for your search (e.g. don't use defaults for short sequences ...
written 2 days ago by
Jean-Karim Heriche ♦ 21k
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C: UpSet R plot using text files
... This is because you're reading the files as csv which stands for "comma-separated values". Adapt the separator argument to match the type of white spaces used in your files. Also header = FALSE means that the first row is going to be treated as data, probably not what you want. Please read [the doc ...
written 4 days ago by
Jean-Karim Heriche ♦ 21k
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... There's also the [Ensembl BLAST/BLAT page][1]. It defaults to human but you can add/remove species.
Note that for short sequences, you may need to adjust blastn parameters away from default values, e.g. decrease word size and increase e-value.
[1]: https://www.ensembl.org/Multi/Tools/Blast ...
written 5 days ago by
Jean-Karim Heriche ♦ 21k
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C: UpSet R plot using text files
... The answer is: read the docs. If the issue can't be solved by this then you need to be more precise about what the issue is. ...
written 5 days ago by
Jean-Karim Heriche ♦ 21k
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... a - Why do you take the geometric mean of the rescaled logs? You can just take the arithmetic mean. Whichever score you get, you can always rescale it to suit your needs.
b - If you want your score to reflect the number of samples, you can start by just taking the sum of the individual scores, not ...
written 6 days ago by
Jean-Karim Heriche ♦ 21k
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... This refers to variants. See this [previous post][1].
By definition, a variant is left aligned if and only if it is no longer possible to shift its position to the left while keeping the length of all its alleles constant. See the [variant normalization page here][2].
[1]: https://www.biostars. ...
written 8 days ago by
Jean-Karim Heriche ♦ 21k
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Answer:
A: Job management programs
... Look into [scientific workflow management systems][1].
[1]: https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems ...
written 10 days ago by
Jean-Karim Heriche ♦ 21k
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For A: Bonferonni Correction for mostly overlapping enhancers
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For C: How to make sure there is no duplicate sequence in a fasta file?
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For A: Determination of hub genes in PPI network
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