Moderator: Jean-Karim Heriche

Reputation:
12,840
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Trusted
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

<prev • 1,659 results • page 1 of 166 • next >
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Comment: C: searching a method for analyzing Differential Expressed Genes instead of constr
... 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 Heriche13k
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Comment: C: Is there any disease mainly caused by underexpression or overexpression of some
... 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 Heriche13k
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Comment: C: Use of uninitialized value error in Perl Script
... 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 Heriche13k
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Comment: C: Correlation among genes in micro array data
... Yes, if you only care about correlation in general, you take all data. ...
written 3 days ago by Jean-Karim Heriche13k
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Answer: A: Correlation among genes in micro array data
... 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 Heriche13k
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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 Heriche13k
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Comment: C: Correlation among genes in micro array data
... 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 Heriche13k
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Answer: A: Blood contamination in RNA-seq analysis
... 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 Heriche13k
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Answer: A: How to download PPI network file from Reactome database for a list of genes and
... 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 Heriche13k
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Answer: A: What is the best tool / method to conduct ongoing curation of research work ?
... 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 Heriche13k

Latest awards to Jean-Karim Heriche

Librarian 23 days ago, created a post with more than 10 bookmarks. For Heatmaps in R
Scholar 26 days ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 4 weeks ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
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?
Appreciated 4 weeks ago, created a post with more than 5 votes. For C: What is a gene transcript?
Appreciated 4 weeks ago, created a post with more than 5 votes. For C: What is a gene transcript?
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?
Commentator 5 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?
Commentator 6 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?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 6 weeks ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Scholar 8 weeks ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Scholar 10 weeks ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Scholar 10 weeks ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Commentator 11 weeks ago, created a comment with at least 3 up-votes. 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, created an answer that has been accepted. 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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