User: b.nota
b.nota • 3.7k
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Posts by b.nota
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Comment:
C: find significant analysis?
... There is also an R package especially for this purpose, [geneOverlap][1].
[1]: https://bioconductor.org/packages/release/bioc/vignettes/GeneOverlap/inst/doc/GeneOverlap.pdf ...
written 3 days ago by
b.nota • 3.7k
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... I think best is to try the default size of `200` first. There is also an option to put `size given`, which means the exact size in your bed file will be used.
Check the manual by only typing in the function name:
findMotifsGenome.pl ...
written 11 days ago by
b.nota • 3.7k
2
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... The difference between `findMotifs.pl` and `findMotifsGenome.pl` is that the first works with gene names (or IDs) as input, and the second with genome coordinates. You have coordinates so you can use `findMotifsGenome.pl`.
For this you need a bed file, I think only the first 4 columns are needed (I ...
written 12 days ago by
b.nota • 3.7k
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... Because for microarrays it is better not to use a t-test but use eBayes moderated t-statistics which is not available in excel, but is available in R limma. ...
written 19 days ago by
b.nota • 3.7k
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... Hi David, I haven't heard back, so I hope no news is good news? If you're still having problem using `gogadget` with non-model organisms, please open a new question with some of your code in it as well, and tag it with `gogadget`. I can help you then with the code adjustment which is probably necess ...
written 5 months ago by
b.nota • 3.7k
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... NEWS 2017/10/27
I recently found out that the `gogadget.gmt` function didn't work properly anymore. Probably the behavior of `dplyr` functions changed, when I (accidentally) updated some packages.
However, this function is fixed in the newest version of `gogadget` v2.1. ...
written 5 months ago by
b.nota • 3.7k
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... Wow, thanks for your hacking solution man. I didn't expect any solution anymore, I thought it was just me. So when my co-workers asked again for the motifs last week, I found out that you can also use the old method in homer (without the svg). You'll have to include `-seqlogo` to the `findMotifsGeno ...
written 5 months ago by
b.nota • 3.7k
1
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... Sad to hear you are still in your mantrum. Good luck with your research endeavors, hope you find a solution for your problem(s) soon. ...
written 6 months ago by
b.nota • 3.7k
2
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... I also asked this question on [SE bioinformatics][1], but since I didn't get any answers yet, I would like to ask it here as well. Hope you don't mind.
I have been using homer's `findMotifsGenome.pl`, but with my new version (v4.9.1) of homer I don't get `.motif` files in the knownResults folder. I ...
written 7 months ago by
b.nota • 3.7k
• updated
5 months ago by
Malcolm.Cook • 790
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Comment:
C: heatmap.2 reorder branches
... Yeah it doesn't work, with reorder function you can only switch two leafs in the same branch. I wanted to switch whole branches containing more leafs per branch.
I have tried your weights approach, but can't find the right settings to get exactly the same branches but then switched.
Thanks anyway ...
written 9 months ago by
b.nota • 3.7k
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