Moderator: Jean-Karim Heriche

Reputation:
7,400
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Trusted
Location:
EMBL Heidelberg, Germany
Website:
http://jkh1.github.io/
Last seen:
4 hours ago
Joined:
5 years, 6 months ago
Email:
h******@embl.de

Posts by Jean-Karim Heriche

<prev • 940 results • page 1 of 94 • next >
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Comment: C: heatmap resolution issue
... Have you tried playing with parameters cellwidth, cellheight, fontzise, fontsize_row and fontsize_col ? ...
written 2 days ago by Jean-Karim Heriche7.4k
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Comment: C: Passing multiple arguments to external programs in a Pipeline with Python
... This looks to me like an advanced python programming question better asked on SO. I am also not sure I quite understand the question but it looks like you could use a lightweight workflow management system like one of [these.][1] [1]: https://github.com/pditommaso/awesome-pipeline ...
written 2 days ago by Jean-Karim Heriche7.4k
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Answer: A: Compare two gene co-expression networks/correlation matrizes
... You can test whether the difference between the two correlation matrices is statistically significant using Jennrich's test implemented in R in the [psych package][1] in function [cortest.jennrich()][2]. Alternatively, an idea for comparing two networks would be to compare the transition matrices of ...
written 2 days ago by Jean-Karim Heriche7.4k
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Comment: C: InterProScan standalone - error connected to non-unique fasta identifiers
... Just add a unique identifier to non-unique fasta headers. It makes sense to stop on non-unique identifiers since if IDs are not unique, you wouldn't be able to unambiguously associate the results with a sequence. ...
written 4 days ago by Jean-Karim Heriche7.4k
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Answer: A: survival analysis using R
... Most likely, you should convert your time variable to a numeric type. It could be as simple as using as.numeric() but it depends on what type your data is. ...
written 5 days ago by Jean-Karim Heriche7.4k
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Comment: C: How can I get Tabular output using HMMer
... The message indicates that you're missing something on your command line. Did you specify an output file after --tblout i.e. --tblout /path/to/output/file ? ...
written 6 days ago by Jean-Karim Heriche7.4k
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Comment: C: problem in extracting sequences
... With base R, it's just a matter of subsetting the data frame. ...
written 6 days ago by Jean-Karim Heriche7.4k
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Answer: A: 3D PCA Plot from RNA-Seq data
... For 3D plots in R, have a look at scatter3d() in the [car package][1], the [scatterplot3d package][2], the [plot3D package][3] or the [rgl package][4]. You'll find introductions to these packages [here][5]. [1]: https://CRAN.R-project.org/package=car [2]: https://CRAN.R-project.org/package=sca ...
written 7 days ago by Jean-Karim Heriche7.4k
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Answer: A: Functional Annotation for sequences
... Use [EnsEMBL][1] if your species is represented there. If [BioMart][2] doesn't give you all you need, you can use the [perl API][3]. [1]: http://www.ensembl.org/index.html [2]: http://www.ensembl.org/biomart [3]: http://www.ensembl.org/info/docs/api/index.html ...
written 7 days ago by Jean-Karim Heriche7.4k
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Answer: A: graph theory with applications to biology/bioinformatics
... [Example][1] of use of kernels on graph nodes. Although not graph theory per se, you may be interested in how dynamic graphs can be analyzed using tensor factorization methods, see some of [my notes here][2]. [1]: http://www.molbiolcell.org/content/25/16/2522.long [2]: http://jkh1.github.io/d ...
written 13 days ago by Jean-Karim Heriche7.4k

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Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 6 days ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
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Popular Question 6 weeks ago, created a question with more than 1,000 views. For Heatmaps in R
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Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
Scholar 5 months ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Scholar 5 months ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?

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