Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan68k
Reputation:
67,570
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
8 hours ago
Joined:
4 years, 3 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 • 7,977 results • page 1 of 798 • next >
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Comment: C: Calculating inner mate distance for paired reads
... Probably not. ...
written 8 hours ago by Devon Ryan68k
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Answer: A: How to generate alignment report from bam files
... That's essentially what `samtools mpileup` is doing, though I certainly hope you're not planning to actually write that out to a file. ...
written 8 hours ago by Devon Ryan68k
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Comment: C: How to perform edgeR based on serial paired samples? (model.matrix design)
... Did you merge your `affected_t1` group with something else? Anyway, prepend `group` to what I wrote and swap `affected` for `treatment`, since you apparently changed the names from your post. **Edit** Silly me, the subject coefficients combine to form `affected_t1`. ...
written 9 hours ago by Devon Ryan68k
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Comment: C: How and what are the steps for performing RNAseq Time point analysis 3 biologica
... Yeah, pretty sure OP's example doesn't actually work. ...
written 9 hours ago by Devon Ryan68k
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Answer: A: GTF file: CDS feature is exon 1, but has frame = 1 or 2
... For genes on the `-` strand, you don't want exon 1, but the last exon. You'll note it has frame 0. ...
written 15 hours ago by Devon Ryan68k
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Comment: C: What is each sequence valid identifier
... Again, such files are so obscure and old (I've never even seen one and I've been doing this for a while) that it's a waste of time to worry about. Sequence identifiers may only start with `@`. Anything else is simply wrong and your program should throw an error. ...
written 16 hours ago by Devon Ryan68k
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Comment: C: How to perform DESeq2 based on paired sample test?
... You're using DESeq2, so `counts(dds, normalized=T)` will give you more useful values. ...
written 16 hours ago by Devon Ryan68k
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Comment: C: How to perform edgeR based on serial paired samples?
... The pairing already took place in the model fit, so unless someone wants to look at per-subject changes it's not going to be mentioned subsequently. ...
written 16 hours ago by Devon Ryan68k
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Answer: A: What is each sequence valid identifier
... All even remotely recent fastq files are comprised of entries each having 4 lines. In theory it's possible to find files that don't comply with this, but it's not worth anyone's time to worry about that. So the first line in the file and every 4th line thereafter is the beginning of a new record. Th ...
written 18 hours ago by Devon Ryan68k
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Comment: C: How to perform DESeq2 based on paired sample test?
... Looking at raw counts is a waste of time, look at normalized counts. ...
written 19 hours ago by Devon Ryan68k

Latest awards to Devon Ryan

Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Difference between chimeric alignments and multiple mapping
Scholar 1 day ago, created an answer that has been accepted. For A: Difference between chimeric alignments and multiple mapping
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Difference between chimeric alignments and multiple mapping
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Difference between chimeric alignments and multiple mapping
Scholar 2 days ago, created an answer that has been accepted. For A: Difference between chimeric alignments and multiple mapping
Scholar 2 days ago, created an answer that has been accepted. For A: Difference between chimeric alignments and multiple mapping
Scholar 3 days ago, created an answer that has been accepted. For A: Difference between chimeric alignments and multiple mapping
Commentator 3 days ago, created a comment with at least 3 up-votes. For C: Confounding Factors In Microarray Analysis
Appreciated 6 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Difference between chimeric alignments and multiple mapping
Appreciated 8 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Commentator 8 days ago, created a comment with at least 3 up-votes. For C: Confounding Factors In Microarray Analysis
Teacher 8 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 8 days ago, created an answer that was upvoted at least 5 times. For A: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
Scholar 9 days ago, created an answer that has been accepted. For A: Difference between chimeric alignments and multiple mapping
Good Answer 10 days ago, created an answer that was upvoted at least 5 times. For A: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
Teacher 10 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 10 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Scholar 10 days ago, created an answer that has been accepted. For A: Group The Data In Python
Teacher 10 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
Scholar 10 days ago, created an answer that has been accepted. For A: Group The Data In Python
Teacher 10 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
Scholar 10 days ago, created an answer that has been accepted. For A: Group The Data In Python
Scholar 10 days ago, created an answer that has been accepted. For A: Group The Data In Python
Scholar 10 days ago, created an answer that has been accepted. For A: Group The Data In Python

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