Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan78k
Reputation:
77,960
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
8 hours ago
Joined:
5 years, 1 month 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 • 9,024 results • page 1 of 903 • next >
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Comment: C: Combine the fastq files
... Thanks. I wonder how relevant this is these days. Do people even do base recalibration anymore? I too haven't done much in the way of variant calling lately, in case you can't tell :) ...
written 8 hours ago by Devon Ryan78k
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Comment: C: What statistical analysis to perform on data from gene expression analysis?
... You've essentially created a network graph based on coexpression/covariation. One can subdivide that graph into covarying sections ("modules") that can then correlate to various things such as phenotypes and treatments. ...
written 8 hours ago by Devon Ryan78k
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Comment: C: STAR Unmapped reads
... Ah Lexogen, that explains things. You're not going to get better then, those libraries produce a fair amount of junk sequence. ...
written 12 hours ago by Devon Ryan78k
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Comment: C: Combine the fastq files
... Is there a lane component to the read group? ...
written 12 hours ago by Devon Ryan78k
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Comment: C: How to extrach gene names and peaks from BedGraph or BigWig files
... BigWig files can't contain gene information, you'll need a BED or GTF file with that. ...
written 12 hours ago by Devon Ryan78k
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Comment: C: Combine the fastq files
... I expect L1/L2 are lanes (renamed from L001 and L002, though I haven't a clue whey they did that). ...
written 12 hours ago by Devon Ryan78k
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Comment: C: What statistical analysis to perform on data from gene expression analysis?
... The WGCNA method to do that would be to look at the degree of module membership, or perhaps correlation between the genes and the module eigengene. ...
written 15 hours ago by Devon Ryan78k
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Comment: C: using two read counting methods with RNA-seq
... Don't mix and match methods for different genes/types of reads, that's a recipe for messing up the downstream analysis. ...
written 15 hours ago by Devon Ryan78k
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Comment: C: using two read counting methods with RNA-seq
... The method used by mmquant is rather odd. It's incredibly unclear what effect including counts for non-existent fusion genes (due to their sharing reads) would have downstream when one is performing differential expression. My primary concern is that this would both lead to an inflated number of tes ...
written 15 hours ago by Devon Ryan78k
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Comment: C: RNA-Seq identify stably expressed genes
... It's unclear if your real question is how to find stably expressed genes or if instead you're just trying to do that so you can normalize your samples appropriately. ...
written 15 hours ago by Devon Ryan78k

Latest awards to Devon Ryan

Teacher 22 hours ago, created an answer with at least 3 up-votes. For A: Bwa Mem: How To Specify The Fastq Phred Format?
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Lowercase Characters In Sequenced Genomes
Scholar 1 day ago, created an answer that has been accepted. For A: How to changing the Branding Title of Galaxy tools
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Lowercase Characters In Sequenced Genomes
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Lowercase Characters In Sequenced Genomes
Scholar 2 days ago, created an answer that has been accepted. For A: How to changing the Branding Title of Galaxy tools
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Lowercase Characters In Sequenced Genomes
Scholar 3 days ago, created an answer that has been accepted. For A: Hisat2 on multiple paired-end input
Scholar 3 days ago, created an answer that has been accepted. For A: differential gene expression analysis
Scholar 3 days ago, created an answer that has been accepted. For A: How to changing the Branding Title of Galaxy tools
Appreciated 5 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 7 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 8 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: Aggregating Gene Expression Across Rows
Scholar 9 days ago, created an answer that has been accepted. For A: How to changing the Branding Title of Galaxy tools
Scholar 10 days ago, created an answer that has been accepted. For A: How to changing the Branding Title of Galaxy tools
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Fields In The Vcf File
Scholar 12 days ago, created an answer that has been accepted. For A: How to changing the Branding Title of Galaxy tools
Appreciated 13 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: Fields In The Vcf File
Scholar 15 days ago, created an answer that has been accepted. For A: How to changing the Branding Title of Galaxy tools
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Fields In The Vcf File
Scholar 17 days ago, created an answer that has been accepted. For A: How to changing the Branding Title of Galaxy tools
Appreciated 17 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: Fields In The Vcf File

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