Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan88k
Reputation:
87,560
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
53 minutes ago
Joined:
5 years, 11 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 • 9,843 results • page 1 of 985 • next >
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Comment: C: HMM and NGS mapping
... Why would direct alignment not work? ...
written 3 hours ago by Devon Ryan88k
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Comment: C: sam file not showing multi mapped reads
... In the case of equally high scoring alignments the result is pseudo-random. ...
written 8 hours ago by Devon Ryan88k
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Comment: C: HMM and NGS mapping
... Do you have access to the homologous sequences themselves? It'd be simple enough to just align to them. With an HMM I suspect you'll have to invent a scoring method for assessing the quality of an "alignment" (really, the probability of a given HMM producing an observed sequence compared to all othe ...
written 1 day ago by Devon Ryan88k
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Comment: C: HMM and NGS mapping
... Why would you want to do that, as opposed to mapping it to the actual transcriptome? ...
written 2 days ago by Devon Ryan88k
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Comment: C: How to merge read count of multiple sample in one fiel to be used for DESeq2 fol
... Have you tried `full_join()` from `dplyr`? ...
written 3 days ago by Devon Ryan88k
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Comment: C: A weird PCA result using a local Galaxy
... This is from plotPCA in deepTools, which unfortunately defaults to not transposing the matrix before computing the PCA (I assume it was done this way originally since the PCA() function in matplotlib doesn't accept matrices with more columns than rows). So in this case the results just indicate that ...
written 3 days ago by Devon Ryan88k
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Answer: A: A weird PCA result using a local Galaxy
... Make sure to set `Transpose Matrix` to `Yes` (it's under `Show advanced options`). The resulting plot will be much more useful (I wish I'd just made that the default). ...
written 3 days ago by Devon Ryan88k
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Answer: A: HTSeq error: local variable 'NH' referenced before assignment
... This appears to be a bug in the version of HTSeq you're using. Your options are one of the following: 1. See if there's a newer version and upgrade (if not, please report this bug to the author). 2. Use a different tool, such as featureCounts from the subread package (this is much faster than htseq ...
written 5 days ago by Devon Ryan88k
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Comment: C: How to prepare "trait.csv" ("trait data") file for creating correlation network
... Then create a text file with that information in it. ...
written 6 days ago by Devon Ryan88k
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Comment: C: batch effect Deseq2 Wald test
... I'm not sure how you got that interpretation, you control it by adding it to your model, just as in an LRT. ...
written 8 days ago by Devon Ryan88k

Latest awards to Devon Ryan

Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Where Is Mirna Binding Site On Mrna ?
Good Answer 4 days ago, created an answer that was upvoted at least 5 times. For A: When should you use SVA vs. ComBat?
Appreciated 6 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: Correlation analysis between gene expression & tumor purity
Scholar 12 days ago, created an answer that has been accepted. For A: Correlation analysis between gene expression & tumor purity
Good Answer 12 days ago, created an answer that was upvoted at least 5 times. For A: When should you use SVA vs. ComBat?
Good Answer 14 days ago, created an answer that was upvoted at least 5 times. For A: When should you use SVA vs. ComBat?
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: Where Is Mirna Binding Site On Mrna ?
Scholar 18 days ago, created an answer that has been accepted. For A: Correlation analysis between gene expression & tumor purity
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: Where Is Mirna Binding Site On Mrna ?
Scholar 23 days ago, created an answer that has been accepted. For A: Correlation analysis between gene expression & tumor purity
Appreciated 25 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Good Answer 25 days ago, created an answer that was upvoted at least 5 times. For A: When should you use SVA vs. ComBat?
Appreciated 27 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Normalizing Rna-Seq Data Using Ercc Spike-In
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: When should you use SVA vs. ComBat?
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: When should you use SVA vs. ComBat?
Appreciated 4 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Normalizing Rna-Seq Data Using Ercc Spike-In
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Normalizing Rna-Seq Data Using Ercc Spike-In
Scholar 5 weeks ago, created an answer that has been accepted. For A: Correlation analysis between gene expression & tumor purity
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: When should you use SVA vs. ComBat?
Appreciated 5 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Scholar 5 weeks ago, created an answer that has been accepted. For A: How To Create A Bigwig File And Display It

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