User: e.rempel
e.rempel • 980
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- Germany, Heidelberg
- Last seen:
- 2 days, 10 hours ago
- Joined:
- 5 years, 9 months ago
- Email:
- e*******@dkfz-heidelberg.de
Statistician/bioinformatician.
Posts by e.rempel
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Comment:
C: About shiny HTML issues
... Sorry, but this is just not enough information. Furthermore, I think, it is more helpful to post this question on stackoverflow. ...
written 5 days ago by
e.rempel • 980
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... So there are two possibilities:
- using absolute path to bedGraphToBigBig: /opt/anaconda3/bin/bedGraphToBigWig
- (better one) add /opt/anaconda3/bin to your PATH (look [this link][1])
[1]: https://unix.stackexchange.com/a/26059 ...
written 7 weeks ago by
e.rempel • 980
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... Interesting that your conda was apparently installed in /opt. One more thing: could you run
find / -name 'bedGraphToBigWig'
You will receive a lot of *Operation not permitted* but if bedGraphToBigWig is installed, we will see where it is. Then we have to adjust your $PATH. ...
written 7 weeks ago by
e.rempel • 980
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724
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... So, your solution was to downgrade R and according packages? ...
written 7 weeks ago by
e.rempel • 980
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... Hi Oli,
you could specify *allGenes* as a factor (length equals number of significant genes in the *background*). This factor equals 1 if the gene is also in * interesting_genes* and 0 otherwise.
background_genes = names(background)[background <= 0.05]
int.genes <- factor(as.integer( ...
written 7 weeks ago by
e.rempel • 980
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... This is really strange, I tried on my computer
conda install -c bioconda ucsc-bedgraphtobigwig
and it worked. It was installed in ~/miniconda3/bin and I could execute "bedGraphToBigWig". One thing you could try (sorry, maybe you have checked it already) whether the path to your conda is in the ...
written 7 weeks ago by
e.rempel • 980
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... From the top of my head, try
ucsc
Followed by TAB button. It could be that the installed commands have “ucsc” prefix ...
written 7 weeks ago by
e.rempel • 980
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... Just a few remarks:
- if you use for loop in one line, the syntax should be different and contain semicolons. Otherwise, you could use indentations.
- if I am not mistaken, the usual input for caseControl is a vcf file with multiple samples in it (meaning multiple sample columns in the vcf file). ...
written 8 weeks ago by
e.rempel • 980
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Comment:
C: GOseq gene2cat format errors
... > I tried the reverse, split(df$GO, df$GO)
is just a typo, right? You have tried split(df$GO, df$gene_id)? ...
written 8 weeks ago by
e.rempel • 980
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... Please, be more elaborate, e.g. provide the code you have tried, the error messages you have obtained, and so on. You would not expect a person to spend more time on the answer than you have spent on writing the question, would you? ...
written 8 weeks ago by
e.rempel • 980
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