Moderator: Jean-Karim Heriche

Reputation:
8,830
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Trusted
Location:
EMBL Heidelberg, Germany
Website:
http://jkh1.github.io/
Last seen:
9 hours ago
Joined:
5 years, 8 months ago
Email:
h******@embl.de

Posts by Jean-Karim Heriche

<prev • 1,119 results • page 1 of 112 • next >
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Answer: A: Linking NCBI gene ID's to nucleotide sequence
... You need to query the gene database not the nucleotide one or find out what is the corresponding identifier in the nucleotide database. ...
written 17 hours ago by Jean-Karim Heriche8.8k
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Comment: C: Is there a consensus that Matlab is the wrong language for open-access bioinform
... The drawback is not so much that it's not open source as the fact that it could be quite expensive. I've also seen a lot of matlab code in papers but, although I am not saying this doesn't exist, I don't remember seeing matlab code in bioinformatics papers I read. In addition, a lot of papers that ...
written 17 hours ago by Jean-Karim Heriche8.8k
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Comment: C: Is there a consensus that Matlab is the wrong language for open-access bioinform
... Matlab is a standard in many CS fields, in particular in engineering and some areas that deal with images. One of the reasons is that these university departments get comparatively cheap licenses. One aspect to consider is interoperability. This is important if your tool is going to be run as part o ...
written 18 hours ago by Jean-Karim Heriche8.8k
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Answer: A: The best way to compare the clusters by different gene sets on the same RNA-Seq
... This is a 4x4 contingency table. Use the Chi-squared test or in your case Fisher's exact test because you have many cells with low counts. ...
written 2 days ago by Jean-Karim Heriche8.8k
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Comment: C: What should we consider when setting up a bioinformatics web service?
... Provide the code in a form useful to the intended target community. Matlab is not very much used in the bioinformatics community. I don't see why you would want users of your code to pay a third party for using it, unless, of course, you have financial interests in the company owning Matlab. Publish ...
written 2 days ago by Jean-Karim Heriche8.8k
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Comment: C: Classifier for Prediction of limited proteolysis from protein structure and sequ
... There's no best classifier as it depends on how you approach the problem. What you should be asking instead is: what is the best prediction accuracy obtained so far and how was it achieved ? For this you'll probably have to read papers on the subject to know what has been tried and get an idea in w ...
written 3 days ago by Jean-Karim Heriche8.8k
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Comment: C: Problem with using "until" in "bash script"
... From that link: > The until loop is very similar to the while loop, except that the loop executes until the TEST-COMMAND executes successfully. As long as this command fails, the loop continues. By the way this is not a bioinformatics question. ...
written 4 days ago by Jean-Karim Heriche8.8k
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Answer: A: NCI-60 dataset in R
... You can download the data at [CellMiner][1]. [1]: https://discover.nci.nih.gov/cellminer/home.do ...
written 4 days ago by Jean-Karim Heriche8.8k
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Answer: A: Publication ethics and authorship guidelines
... First thing, do not publish without all authors consent, this would not end well. Also do not publish without giving appropriate credit where it is due, i.e. do not omit from the author's list people who made significant contributions. This is unethical. You may be able to get away with it but these ...
written 4 days ago by Jean-Karim Heriche8.8k
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Comment: C: What are advantages of using Gene Regualtory Networks over Statistical methods w
... Gene regulatory networks inference is based on statistical methods so what you're asking is not entirely clear to me. Usually the process is to first identify lists of genes that are differentially expressed then in a second step try to infer from this a network of regulation. I suggest you take a ...
written 4 days ago by Jean-Karim Heriche8.8k

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Scholar 17 hours ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
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Scholar 21 days ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
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