Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan96k
Reputation:
95,880
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
19 hours ago
Joined:
7 years, 4 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 • 10,318 results • page 2 of 1032 • next >
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Comment: C: featureCounts for paired bam files and dealing with multimapping reads?
... We still ignore multimappers if your tool needs integers. ...
written 12 days ago by Devon Ryan96k
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3
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Comment: C: Extract gene coordinates from GTF
... You'd need to script something. ...
written 14 days ago by Devon Ryan96k
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Comment: C: Is removing rRNA a necessary step in RNA-seq?
... No, if you don't care about them then you should remove the counts from the matrix. Otherwise you're needless inflating the tests you're doing and deflating your power. The normalization should be robust to their presence, but if there's a LOT of rRNA contamination in one sample then that tends to c ...
written 17 days ago by Devon Ryan96k
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Answer: A: How to make it significant
... meaninglessTest <- function(x) { return(sum(x[4:6]) - sum(x[1:3]) > 0) } That is a meaningless test that will return `true` that there's a difference. No proper statistical test will be significant for that comparison with only 3 samples. Your goal is also not to show there's ...
written 17 days ago by Devon Ryan96k
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1
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Comment: C: how to extract intron coordinates (in bed) from bam
... You need to tell your aligner and stringTie that. ...
written 19 days ago by Devon Ryan96k
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106
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Comment: C: Converting scRNA-Seq to Bulk-RNASeq
... The term you're looking for is "pseudo bulk" and you'll want to sum values across cells. ...
written 20 days ago by Devon Ryan96k
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Comment: C: How to find the differences in aligned bam files
... RPGC, the online documentation you're looking at is for the current version. You might switch to using conda on your HPC so you're not reliant on the system administrators to constantly do that. ...
written 20 days ago by Devon Ryan96k
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Comment: C: Featurecounts to DESEq2 - How to merge biological replicates?
... Combine read.delim with lapply. Have a look at how readDGE works internally. ...
written 20 days ago by Devon Ryan96k
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Answer: A: type='apeglm' shrinkage only for use with 'coef'
... Set `type` to something else, such as `normal` or `ashr`. ...
written 22 days ago by Devon Ryan96k
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Comment: C: how to extract intron coordinates (in bed) from bam
... Then you can't know which strand the transcripts are from. ...
written 23 days ago by Devon Ryan96k

Latest awards to Devon Ryan

Teacher 20 hours ago, created an answer with at least 3 up-votes. For A: How To Write Data In A Granges Object To A Bed File.
Scholar 20 hours ago, created an answer that has been accepted. For A: Making a Model Matrix for Anova-like analysis
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: How To Write Data In A Granges Object To A Bed File.
Scholar 4 days ago, created an answer that has been accepted. For A: Making a Model Matrix for Anova-like analysis
Good Answer 4 days ago, created an answer that was upvoted at least 5 times. For A: How To Write Data In A Granges Object To A Bed File.
Commentator 12 days ago, created a comment with at least 3 up-votes. For C: Perl Script To Make Statistics Of Mirna Abundances For Many Samples
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: How To Write Data In A Granges Object To A Bed File.
Good Answer 12 days ago, created an answer that was upvoted at least 5 times. For A: How To Write Data In A Granges Object To A Bed File.
Good Answer 14 days ago, created an answer that was upvoted at least 5 times. For A: R - pheatmap - changing column order
Good Answer 14 days ago, created an answer that was upvoted at least 5 times. For A: How To Write Data In A Granges Object To A Bed File.
Appreciated 14 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Scholar 17 days ago, created an answer that has been accepted. For A: Making a Model Matrix for Anova-like analysis
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: How To Write Data In A Granges Object To A Bed File.
Scholar 17 days ago, created an answer that has been accepted. For A: Making a Model Matrix for Anova-like analysis
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: How To Write Data In A Granges Object To A Bed File.
Appreciated 18 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 23 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: filtering paired end mapped reads form SAM/BAM file
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Making a Model Matrix for Anova-like analysis
Scholar 27 days ago, created an answer that has been accepted. For A: Making a Model Matrix for Anova-like analysis
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Making a Model Matrix for Anova-like analysis
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Making a Model Matrix for Anova-like analysis
Appreciated 4 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Making a Model Matrix for Anova-like analysis

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