User: b.nota

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b.nota3.7k
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Posts by b.nota

<prev • 568 results • page 1 of 57 • next >
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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.nota3.7k
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Comment: C: How to add Unique Peak ID to a bed file created from MACS for HOMER analysis
... 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.nota3.7k
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Answer: A: How to add Unique Peak ID to a bed file created from MACS for HOMER analysis
... 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.nota3.7k
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Comment: C: P-value calculation for gene expression data
... 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.nota3.7k
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Comment: C: gogadget: an R package for go analysis visualization and interpretation
... 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.nota3.7k
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Answer: A: gogadget: an R package for go analysis visualization and interpretation
... 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.nota3.7k
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Comment: C: Where are .motif files from homer knownResults?
... 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.nota3.7k
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Comment: C: Is PatScan RNA pattern searcher no longer available as an online webtool?
... 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.nota3.7k
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Where are .motif files from homer knownResults?
... 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 ...
homer chip-seq atac-seq motifs written 7 months ago by b.nota3.7k • updated 5 months ago by Malcolm.Cook790
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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.nota3.7k

Latest awards to b.nota

Scholar 12 days ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Bioinformatics freelancers needed
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: RNA to protein in bash?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Blasting against multiple fasta file
Scholar 4 months ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
Popular Question 5 months ago, created a question with more than 1,000 views. For Find genes of enriched known motif results in HOMER
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Appreciated 6 months ago, created a post with more than 5 votes. For A: Bioinformatics freelancers needed
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Blasting against multiple fasta file
Scholar 8 months ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
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Commentator 10 months ago, created a comment with at least 3 up-votes. For C: RNA to protein in bash?
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Fastest pairwise alignment for 10,000 sequences
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Scholar 10 months ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
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