Moderator: Jean-Karim Heriche

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Location:
EMBL Heidelberg, Germany
Website:
http://jkh1.github.io/
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Joined:
7 years, 8 months ago
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Posts by Jean-Karim Heriche

<prev • 2,201 results • page 1 of 221 • next >
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Answer: C: Render GEO data in R shiny mainpanel
... This is an R/Shiny programming question not a bioinformatics one even if it's applied to a bioinformatics data set. Your code is not structured as a Shiny app. Start by reading the [Shiny tutorial][1]. [1]: https://shiny.rstudio.com/articles/ ...
written 1 day ago by Jean-Karim Heriche18k
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Comment: C: Is there a public database containing Sanger sequencing trace files?
... Are you specifically after AB1 files or traces ? If the later, the [European Nucleotide Archive stores traces][1] but not as AB1 files. [1]: https://www.ebi.ac.uk/ena/submit/trace-format ...
written 5 days ago by Jean-Karim Heriche18k
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Comment: C: R Problem - Save variables
... This is not really a bioinformatics question and may be better directed at StackOverflow. Anyways, one option would be to pass the file name as an argument to the script so that each run gets a different one, for example based on job array index. ...
written 9 days ago by Jean-Karim Heriche18k
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Comment: C: Some question in Hmmer package
... It seems that you're looking for a well defined motif. In this case, you could just search using regular expressions, e.g. /[T|A]TTGA.{5}TT[G|A]/g assuming the occurrences are non overlapping in which case, you probably can use look arounds like /(?= [T|A]TTGA.{5}TT[G|A])/g. ...
written 13 days ago by Jean-Karim Heriche18k
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Answer: A: How to retrieve all GO terms at level 2 from a list input
... You have several options: - use [owltools][1] - use [go-perl][2] - use the Bioconductor package [GO.db][3] [1]: https://github.com/owlcollab/owltools [2]: https://metacpan.org/pod/distribution/go-perl/go-perl.pod [3]: https://bioconductor.org/packages/release/data/annotation/html/GO.db ...
written 13 days ago by Jean-Karim Heriche18k
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Comment: C: Sorting of patterns and their representation with R
... It looks to me like you're trying to do something similar to sequence logos. Check these options: - Bioconductor [seqLogo package][1] - [ggseqlogo package][2] - this [blog][3] [1]: https://bioconductor.org/packages/release/bioc/html/seqLogo.html [2]: https://omarwagih.github.io/ggseqlo ...
written 14 days ago by Jean-Karim Heriche18k
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Answer: A: N:M or 1:M relationship?
... N:M means a many-to-many relation and 1:N means a one-to-many relation. Since a sample can have multiple indexes, the index side is N and since an index can be used for more than one sample then the sample side should be >=1 so M. So you need to represent a N:M/many-to-many relationship. ...
written 16 days ago by Jean-Karim Heriche18k
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Comment: C: are known polymorphisms in the primer sequence?
... And you can also do the same with Ensembl BLAST. ...
written 17 days ago by Jean-Karim Heriche18k
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Answer: A: Cytoscape - disproportionately big files
... Most likely this has to do with compression. Compression doesn't always reduce file size. Compression typically makes use of redundant information. By removing networks, some information that was redundant may not be anymore and thus harder to compress. ...
written 23 days ago by Jean-Karim Heriche18k
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Answer: A: Question regarding R software
... Try [ComplexHeatmap][1]. [Here is the tutorial][2]. Otherwise, check other [options here][3]. [1]: https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html [2]: https://jokergoo.github.io/ComplexHeatmap-reference/book/ [3]: https://www.biostars.org/p/205417/ ...
written 23 days ago by Jean-Karim Heriche18k

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Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Rnai Screening Data Repositories?
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Scholar 9 weeks ago, created an answer that has been accepted. For A: Bonferonni Correction for mostly overlapping enhancers
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