Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan93k
Reputation:
93,230
Status:
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Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
23 hours ago
Joined:
6 years, 10 months ago
Email:
d*******@gmail.com

I'm currently a bioinformatician/data manager at the Max Planck Institute for Immunobiology and Epigenetics in Freiburg, Germany.

I was a post-doc at the DZNE in Bonn, Germany, spending much of my time working on epigenetics and NGS.

Posts by Devon Ryan

<prev • 10,180 results • page 1 of 1018 • next >
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Comment: C: In PCA on RNA-Seq data, what does Gaussian distribution refer to?
... PCA necessarily finds independent factors, that's literally how it works. Those may or may not be related to anything biologically relevant, of course. ICA is a bit harder to compute and generally of lower utility except when you KNOW that the resulting components have a biological interpretation. A ...
written 1 day ago by Devon Ryan93k
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Comment: C: Length of differentially methylated regions
... One normally allows distance in between, though 2kb would be biologically excessive. You will not find a reference to 3 CpGs in any paper, it's not something people write down. ...
written 1 day ago by Devon Ryan93k
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Answer: A: In PCA on RNA-Seq data, what does Gaussian distribution refer to?
... The data does not need to be Gaussian and RNA-seq data is not Gaussian unless you want to transform it. PCA has more utility (in that the results look nicer) when you can transform the data such that there's Gaussian variance across genes, but that isn't a requirement. ...
written 1 day ago by Devon Ryan93k
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Comment: C: allen brain atlas data extraction
... Have you looked at their data portal? http://mouse.brain-map.org/static/download ...
written 1 day ago by Devon Ryan93k
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Comment: C: Genomic Restriction Finder
... You're looking for https://github.com/lindenb/jvarkit ...
written 1 day ago by Devon Ryan93k
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Comment: C: Normalizing NGS samples expected to have different total reads
... This sort of scenario is really worst-case for MeDIP. The best you can do is find those regions with some notable amount of coverage in the KO samples and normalize only using them. This presumes, of course, that those regions weren't affected by the KO, which may not be true, but it's the best that ...
written 2 days ago by Devon Ryan93k
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Comment: C: DEseq2 tool on Galaxy software problems regarding normalization of featurecounts
... You might want to ask about Galaxy on the Galaxy support site, it's not heavily used by the regulars here. ...
written 5 days ago by Devon Ryan93k
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Comment: C: Do you need a deduplication tool for FASTQ data in fastp?
... They've recently added a [gencore repository](https://github.com/OpenGene/gencore), which might be able to do that. I haven't used this yet, I just remember merging in the bioconda recipes recently. Update: I guess this takes BAM files, so it's not relevant. ...
written 6 days ago by Devon Ryan93k
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Comment: C: DEseq2 tool on Galaxy software problems regarding normalization of featurecounts
... How did you compute the normalized counts in edgeR? Likely there was an error there, since there's no equivalent to `counts(dds, normalized=T)` in edgeR. ...
written 6 days ago by Devon Ryan93k
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Job: Bioinformatician in a core facility (MPI-IE, Freiburg Germany). Permanent position!
... We have [an opening in our core facility](https://www.ie-freiburg.mpg.de/5197180/job_full_offer_14345720) starting in March for a bioinformatician. The contract is originally for two year and thereafter becomes permanent. This is a replacement for me (I'm moving into the private sector), so please f ...
core facility job written 7 days ago by Devon Ryan93k

Latest awards to Devon Ryan

Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Script To Calculate Length Distribution Of A Collapsed Fasta File
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Script To Calculate Length Distribution Of A Collapsed Fasta File
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: Script To Calculate Length Distribution Of A Collapsed Fasta File
Appreciated 12 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 12 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Scholar 12 days ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Appreciated 14 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Scholar 16 days ago, created an answer that has been accepted. For A: unit scale in plotprofile plot - deeptools2
Scholar 16 days ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Script To Calculate Length Distribution Of A Collapsed Fasta File
Scholar 19 days ago, created an answer that has been accepted. For A: unit scale in plotprofile plot - deeptools2
Scholar 19 days ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Scholar 20 days ago, created an answer that has been accepted. For A: unit scale in plotprofile plot - deeptools2
Scholar 20 days ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Scholar 20 days ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Scholar 22 days ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Scholar 22 days ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Difference between abundance and counts in RNA-Seq
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Difference between abundance and counts in RNA-Seq
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Script To Calculate Length Distribution Of A Collapsed Fasta File
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Script To Calculate Length Distribution Of A Collapsed Fasta File
Scholar 6 weeks ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Script To Calculate Length Distribution Of A Collapsed Fasta File

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