Moderator: Jean-Karim Heriche

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EMBL Heidelberg, Germany
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http://jkh1.github.io/
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Posts by Jean-Karim Heriche

<prev • 2,056 results • page 1 of 206 • next >
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Comment: C: Making row and column names visible on heatmap.
... See also this [previous post][1] listing various heatmap packages and links to tutorials. As mentioned, typically, one makes text readable by controlling both the plot and the text sizes. [1]: https://www.biostars.org/p/205417/ ...
written 11 days ago by Jean-Karim Heriche16k
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Comment: C: "missing value where TRUE/FALSE needed" in 16Stimator R script
... If you're using Rstudio, you could just click on Df16S in the list of objects in your environment or type View(Df16S) in the console. In an R terminal, you just type Df16S and the top 100 or so rows would be displayed. A common debugging technique is to output the variable value just before the line ...
written 12 days ago by Jean-Karim Heriche16k
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Answer: A: "missing value where TRUE/FALSE needed" in 16Stimator R script
... The error means that the evaluation of the comparison produced an NA value instead of TRUE or FALSE. Since the right hand side of the comparison is a constant, it means that Df16S$GeneLen[r] is most likely not what you think it is. Check what Df16S contains. ...
written 12 days ago by Jean-Karim Heriche16k
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Comment: C: Does mitotic activity inversely correlate with HiC interactions data?
... HiC gives you an idea of the structure of the genome. Unless you know how to correlate particular features of genome architecture to cell density, I don't see how HiC could inform on cell density. ...
written 12 days ago by Jean-Karim Heriche16k
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Answer: A: What is the difference between this Biomart Code, Org.Hs.Db code and SQL code?
... The first one uses Ensembl's biomart whereas the third one directly queries the GO MySQL database. Ensembl has a different set of annotations than GO. It used to be doing its own annotations but maybe now uses GO but with a lag in time which means an older version than the current GO. org.Hs.eg.db a ...
written 13 days ago by Jean-Karim Heriche16k
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Answer: A: Does mitotic activity inversely correlate with HiC interactions data?
... By mitotic activity, I assume you mean the cell(s) being in mitosis otherwise, please clarify what you mean by this. As chromosomes are condensed in mitosis, you expect to see more short range interactions and no particular structure compared to interphase. You may want to have a look at this [paper ...
written 13 days ago by Jean-Karim Heriche16k
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Comment: C: GO(Gene Ontology) IDs for Homo sapiens in all three ontologies
... The Gene Ontology is generally species-agnostic so you should clarify what you mean. Are you looking for all GO terms that are currently used to annotate human genes ? If so, used in which resource ? ...
written 14 days ago by Jean-Karim Heriche16k
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Comment: C: Why learn programming in bioinformatics?
... No tool will cover all possibilities. If your data is in a non-standard format or supposed to be in a standard format but contains formatting errors, these things will have to be fixed on a case-by-case basis as it is unlikely that existing tools will be tailored to your specific issue. Another exam ...
written 15 days ago by Jean-Karim Heriche16k
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Comment: C: Why learn programming in bioinformatics?
... Please use the 'add comment' button to reply to an answer. This keeps things organized and prevents the question to appear as answered when it is not. ...
written 15 days ago by Jean-Karim Heriche16k
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Answer: A: Why learn programming in bioinformatics?
... Ready-to-use tools (online or not) won't do everything for you. For example, a tool would only accept data in a particular format and your data is structured in a non-standard way that no tool knows about so you'll have to write a conversion tool yourself. Or you need to clean up your data before pr ...
written 15 days ago by Jean-Karim Heriche16k

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