Moderator: Jean-Karim Heriche
Jean-Karim Heriche ♦ 13k
- Reputation:
- 12,840
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- Location:
- EMBL Heidelberg, Germany
- Website:
- http://jkh1.github.io/
- Last seen:
- 3 hours ago
- Joined:
- 6 years, 3 months ago
- Email:
- h******@embl.de
Posts by Jean-Karim Heriche
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... Data analysis is best done to answer a question. What kind of data do you have and what question are you trying to address with it ? ...
written 21 hours ago by
Jean-Karim Heriche ♦ 13k
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... Plus cases where pathogens modulate the host's gene/protein expression patterns, e.g. viruses that modulate cytokines expression levels. ...
written 3 days ago by
Jean-Karim Heriche ♦ 13k
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... What's the question ?
The error message is pretty clear. The variable $qulen is not defined, i.e. has no value so you can't use it in a division. Now if you want to find out why you're getting this error, check where this variable is supposed to be initialized:
`my $qulen = length($qseqs{$query}) ...
written 3 days ago by
Jean-Karim Heriche ♦ 13k
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... Yes, if you only care about correlation in general, you take all data. ...
written 3 days ago by
Jean-Karim Heriche ♦ 13k
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... To find disease-specific modules, one approach would be to build two networks, one for healthy and one for disease then try and find the modules that differ between them. For this, you could use a tensor factorization approach based on the CP decomposition. For more details, see my [tutorial on the ...
written 3 days ago by
Jean-Karim Heriche ♦ 13k
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Comment:
C: Replication timing analysis
... This looks taken from a paper. It might help if you provide a link to this paper. ...
written 3 days ago by
Jean-Karim Heriche ♦ 13k
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... It depends on the question you want to address with this. Pearson's correlation tells you how strong the linear relationship is between the expression levels of two genes. In which context are you interested in this ? Do you want to know if two genes are correlated in general or in healthy people on ...
written 3 days ago by
Jean-Karim Heriche ♦ 13k
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... To rephrase @genomax' comment, if the starting material is contaminated, any downstream analysis will be suspect. Unless you can restrict your analysis to sequences that are guaranteed not to be present in blood, I don't see how you could clean up the data and remove any doubt about the final result ...
written 5 days ago by
Jean-Karim Heriche ♦ 13k
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... You may be interested in the [Reactome cytoscape plugin][1]. Have a look at the [documentation on the Reactome wiki][2].
[1]: http://apps.cytoscape.org/apps/reactomefiplugin
[2]: https://wiki.reactome.org/index.php/ReactomeFIViz ...
written 5 days ago by
Jean-Karim Heriche ♦ 13k
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... I am not entirely sure what you're asking about but it seems that you may be interested in notebooks such as provided by [Jupyter][1], [Rstudio][2] or [Beaker][3],
[1]: http://jupyter-notebook-beginner-guide.readthedocs.io/en/latest/what_is_jupyter.html
[2]: http://rmarkdown.rstudio.com/r_note ...
written 5 days ago by
Jean-Karim Heriche ♦ 13k
Latest awards to Jean-Karim Heriche
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26 days ago,
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For A: Bonferonni Correction for mostly overlapping enhancers
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28 days ago,
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For A: Rnai Screening Data Repositories?
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4 weeks ago,
created an answer that has been accepted.
For A: Bonferonni Correction for mostly overlapping enhancers
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For A: Normalized Smith-Waterman Formula
Scholar
4 weeks ago,
created an answer that has been accepted.
For A: Bonferonni Correction for mostly overlapping enhancers
Teacher
4 weeks ago,
created an answer with at least 3 up-votes.
For A: Rnai Screening Data Repositories?
Good Answer
4 weeks ago,
created an answer that was upvoted at least 5 times.
For A: Normalized Smith-Waterman Formula
Scholar
4 weeks ago,
created an answer that has been accepted.
For A: Bonferonni Correction for mostly overlapping enhancers
Teacher
4 weeks ago,
created an answer with at least 3 up-votes.
For A: Rnai Screening Data Repositories?
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For C: How to make sure there is no duplicate sequence in a fasta file?
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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: Rnai Screening Data Repositories?
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6 weeks ago,
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For A: Rnai Screening Data Repositories?
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6 weeks ago,
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For A: Bonferonni Correction for mostly overlapping enhancers
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For A: Bonferonni Correction for mostly overlapping enhancers
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10 weeks ago,
created an answer that has been accepted.
For A: Bonferonni Correction for mostly overlapping enhancers
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10 weeks ago,
created an answer that has been accepted.
For A: Bonferonni Correction for mostly overlapping enhancers
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For C: Is Software Development a key part of Bioinformatics?
Commentator
11 weeks ago,
created a comment with at least 3 up-votes.
For C: How to make sure there is no duplicate sequence in a fasta file?
Scholar
11 weeks ago,
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For A: Bonferonni Correction for mostly overlapping enhancers
Scholar
11 weeks ago,
created an answer that has been accepted.
For A: Bonferonni Correction for mostly overlapping enhancers
Teacher
11 weeks ago,
created an answer with at least 3 up-votes.
For A: Rnai Screening Data Repositories?
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