Moderator: Jean-Karim Heriche
Jean-Karim Heriche ♦ 18k
- Reputation:
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- EMBL Heidelberg, Germany
- Website:
- http://jkh1.github.io/
- Last seen:
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- Joined:
- 7 years, 8 months ago
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Posts by Jean-Karim Heriche
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... 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 Heriche ♦ 18k
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... 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 Heriche ♦ 18k
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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 Heriche ♦ 18k
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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 Heriche ♦ 18k
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... 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 Heriche ♦ 18k
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... 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 Heriche ♦ 18k
2
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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 Heriche ♦ 18k
0
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2
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114
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... And you can also do the same with Ensembl BLAST. ...
written 17 days ago by
Jean-Karim Heriche ♦ 18k
0
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1
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89
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... 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 Heriche ♦ 18k
2
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1
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104
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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 Heriche ♦ 18k
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