Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan63k
Reputation:
62,690
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
12 hours ago
Joined:
4 years 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 • 7,512 results • page 1 of 752 • next >
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Comment: C: bismark methylation extractor for PE reads
... My interpretation is that NGS-Newbie really wants phased methylation status (presumably to make those closed/open circle style plots (do those have a name?) that you often see). ...
written 12 hours ago by Devon Ryan63k
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Comment: C: Is there a consensus that Matlab is the wrong language for open-access bioinform
... Depending on the exactly subpopulation of bioinformatics/biology you're targeting it could well be a lot. At least for those of us involved in NGS, matlab is simply never used for anything. I used it a bit to try out some signal deconvolution methods and other than that the only time I see it used i ...
written 12 hours ago by Devon Ryan63k
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Comment: C: bismark methylation extractor for PE reads
... Out of curiosity, why would you want that? ...
written 1 day ago by Devon Ryan63k
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Answer: A: Does all assemble genome stats available on NCBI are at haploid level ?
... I've only ever seen haploid versions of genomes posted to NCBI. Note that genes numbers don't change since there's an implied 2x copy number. Report genome sizes as haploid for the sake of consistency. ...
written 1 day ago by Devon Ryan63k
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Comment: C: Bowtie2 throws error no. 139
... Weird, this is totally a bowtie2 bug then. Glad you at least got your alignments! ...
written 3 days ago by Devon Ryan63k
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Comment: C: cuffdiff vs cuffnorm vs cuffquant
... I'd prefer to use salmon or kallisto followed by edger or a similar tool, they're inevitably easier to debug. ...
written 3 days ago by Devon Ryan63k
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Comment: C: Meaning of r-MATS results
... I can't honestly recall if they're listed or not, though it would make no sense to do so. ...
written 3 days ago by Devon Ryan63k
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Comment: C: Resources for converting between UCSC <-> Gencode <-> Ensembl chromosome names
... The original information comes from the genome assemblies deposited in NCBI. There are multiple names for each contig therein. The trick is simply to figure out who uses which column (sometimes they like to modify them further). ...
written 6 days ago by Devon Ryan63k
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Comment: C: What to do with read sequence quality
... The answer to this is based entirely on what you're doing. In general, if you don't know the answer to this you probably shouldn't be writing a tool that might need to know it. ...
written 9 days ago by Devon Ryan63k
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Comment: C: Get introns in bam format from alignment reads result
... What is your actual end goal? ...
written 9 days ago by Devon Ryan63k

Latest awards to Devon Ryan

Appreciated 9 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 10 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: R: Merge Duplicates In Column In Data.Frame By Condition In Another Column
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: R: Merge Duplicates In Column In Data.Frame By Condition In Another Column
Appreciated 14 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Good Answer 17 days ago, created an answer that was upvoted at least 5 times. For A: How to extract unique mapped results from Bowtie2 bam results?
Appreciated 18 days ago, created a post with more than 5 votes. For Replace me: bioinformatician/post-doc at the DZNE (Bonn, Germany)
Appreciated 18 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: R: Merge Duplicates In Column In Data.Frame By Condition In Another Column
Good Answer 21 days ago, created an answer that was upvoted at least 5 times. For A: How to extract unique mapped results from Bowtie2 bam results?
Scholar 25 days ago, created an answer that has been accepted. For A: Group The Data In Python
Appreciated 28 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Scholar 29 days ago, created an answer that has been accepted. For A: Group The Data In Python
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Will you critique/rate my mRNA seq alignment analysis?
Scholar 4 weeks ago, created an answer that has been accepted. For A: Group The Data In Python
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: R: Merge Duplicates In Column In Data.Frame By Condition In Another Column
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: R: Merge Duplicates In Column In Data.Frame By Condition In Another Column
Scholar 4 weeks ago, created an answer that has been accepted. For A: Group The Data In Python
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: R: Merge Duplicates In Column In Data.Frame By Condition In Another Column
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: R: Merge Duplicates In Column In Data.Frame By Condition In Another Column
Scholar 5 weeks ago, created an answer that has been accepted. For A: Group The Data In Python
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: How to extract unique mapped results from Bowtie2 bam results?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Group The Data In Python
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: R: Merge Duplicates In Column In Data.Frame By Condition In Another Column
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: Will you critique/rate my mRNA seq alignment analysis?

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