Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan76k
Reputation:
75,620
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
10 hours ago
Joined:
4 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

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Comment: C: RNA-Seq DGE: Evaluate model quality
... The issue is mostly that each gene has its own AIC/BIC. The normal model comparison metrics aren't intended for cases where you're applying that model independently to 30,000 datasets. In general, one uses the simplest possible model that reasonably describes the model (fun fact: if you add enough ...
written 15 hours ago by Devon Ryan76k
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Answer: A: RNA-Seq DGE: Evaluate model quality
... I'm not sure why you bothered expending the effort to use SVA and add principal components as covariates. Unsurprisingly, you have a family effect that you need to account for. So `~family + condition` is the logical first (and probably only) model to use given that. ...
written 16 hours ago by Devon Ryan76k
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Answer: A: Detection of transcripts from mRNA and sRNA
... The ideal procedure would be to concatenate the two genomes and align to that. ...
written 16 hours ago by Devon Ryan76k
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Comment: C: boxplot in edgeR
... I'd like to hear the accent where Kevin/Devon sound like selenocysteine :) ...
written 1 day ago by Devon Ryan76k
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Comment: C: subset gtf file based on coordinates
... You'll want to subset the GRangesList object, that way the gene as a whole will get selected. You shouldn't need to sort things (OK, maybe the seqlevels, I always forget about them). Make sure to export the .grl one. ...
written 1 day ago by Devon Ryan76k
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Comment: C: Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
... There's presumably an extra space somewhere (or in that version maybe `-q` is doing something different). ...
written 1 day ago by Devon Ryan76k
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Comment: C: boxplot in edgeR
... Try a violin or joy plot rather than a box plot. ...
written 1 day ago by Devon Ryan76k
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Comment: C: Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
... You'll want `-s reverse` I think. You can strip `chr` characters with `sed`. ...
written 2 days ago by Devon Ryan76k
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Comment: C: How to extract bigWig signal for a given bed file?
... There's nothing special about the minus strand, it has the same values in a bigWig file. ...
written 2 days ago by Devon Ryan76k
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Comment: C: Problems with macs2
... So does it just not finish ever or what? I've actually seen that happen on occasion, never figured out why though. ...
written 3 days ago by Devon Ryan76k

Latest awards to Devon Ryan

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Fpkm To Transcript Quantification
Scholar 4 days ago, created an answer that has been accepted. For A: Hisat2 on multiple paired-end input
Scholar 4 days ago, created an answer that has been accepted. For A: Hisat2 on multiple paired-end input
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Fpkm To Transcript Quantification
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Fpkm To Transcript Quantification
Scholar 5 days ago, created an answer that has been accepted. For A: Hisat2 on multiple paired-end input
Scholar 6 days ago, created an answer that has been accepted. For A: Hisat2 on multiple paired-end input
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Where Is Mirna Binding Site On Mrna ?
Scholar 8 days ago, created an answer that has been accepted. For A: Hisat2 on multiple paired-end input
Scholar 9 days ago, created an answer that has been accepted. For A: Hisat2 on multiple paired-end input
Good Answer 9 days ago, created an answer that was upvoted at least 5 times. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Where Is Mirna Binding Site On Mrna ?
Appreciated 9 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Where Is Mirna Binding Site On Mrna ?
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Scholar 10 days ago, created an answer that has been accepted. For A: Hisat2 on multiple paired-end input
Good Answer 10 days ago, created an answer that was upvoted at least 5 times. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Appreciated 10 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
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Scholar 14 days ago, created an answer that has been accepted. For A: Hisat2 on multiple paired-end input
Scholar 15 days ago, created an answer that has been accepted. For A: Hisat2 on multiple paired-end input
Good Answer 15 days ago, created an answer that was upvoted at least 5 times. For A: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
Scholar 15 days ago, created an answer that has been accepted. For A: Hisat2 on multiple paired-end input
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Normalizing Rna-Seq Data Using Ercc Spike-In

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