Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan82k
Reputation:
82,470
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
an hour ago
Joined:
5 years, 5 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 • 9,429 results • page 1 of 943 • next >
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Comment: C: htseq-count error utf-8 codec can't decode
... No one has tested anything in python 3.7, try using 3.6 or another non-bleeding edge version. ...
written 1 hour ago by Devon Ryan82k
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Comment: C: DESeq2 using samples with different unique alignment rates
... OK, from that it's clear that rRNA contamination is not a main driver of any of the clustering. I wouldn't worry about incorporating that into your design then. If you need to do that in the future then ensuring it's a continuous variable will probably solve the error message you received. ...
written 3 hours ago by Devon Ryan82k
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Comment: C: Search for gene variants
... You might just update your post with that or a variant of what I wrote in a comment. The replies will probably be more useful then :) ...
written 3 hours ago by Devon Ryan82k
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Comment: C: Search for gene variants
... Can the post essentially be rephrased as the following? > Biologists and clinicians are often faced with searching the literature for a set of given gene variants. There are a number of possible routes they could take, from using specialized databases (odd are they don't know about these) to sim ...
written 4 hours ago by Devon Ryan82k
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Comment: C: htseq-count error utf-8 codec can't decode
... There's probably a special character on line 8700 of the GTF file, have a look around there. ...
written 7 hours ago by Devon Ryan82k
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Comment: C: DESeq2 using samples with different unique alignment rates
... Please color that by rRNA level rather than group. ...
written 7 hours ago by Devon Ryan82k
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Comment: C: DESeq2 using samples with different unique alignment rates
... Does a PCA plot indicate any significant difference in the high rRNA samples? ...
written 9 hours ago by Devon Ryan82k
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Comment: C: quantitative real-time PCR analysis of mRNA expression data
... Real-time PCR validates that the change you see is real in a larger number of additional samples. Whether a change is actually important requires you to understand the underlying biology. You should spend a few days reading the literature related to the research project. ...
written 10 hours ago by Devon Ryan82k
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Comment: C: Deseq2: What is the most correct experimental design for this experiment?
... OK, in that case you don't actually need to model `time`. I'm assuming you did your library preparation/RNA extraction at a single time point rather than as you made the cell lines, since in my experience that can create a significant batch effect. ...
written 13 hours ago by Devon Ryan82k
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Comment: C: Deseq2: What is the most correct experimental design for this experiment?
... If `time` is really not affecting anything then yes you can remove it, it's just that in the design you showed it's mathematically impossible to tell any difference between it and the cell types. What does `time` actually represent here? ...
written 14 hours ago by Devon Ryan82k

Latest awards to Devon Ryan

Teacher 14 hours ago, created an answer with at least 3 up-votes. For C: Error at the end of HT-seq Analysis and output.txt with 0 bytes in size
Scholar 14 hours ago, created an answer that has been accepted. For A: logCPM to RPKM
Teacher 1 day ago, created an answer with at least 3 up-votes. For C: Error at the end of HT-seq Analysis and output.txt with 0 bytes in size
Appreciated 4 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Scholar 5 days ago, created an answer that has been accepted. For A: Microarray Probesets Quality Control - Why exclude non-autosomal probesets?
Scholar 5 days ago, created an answer that has been accepted. For A: logCPM to RPKM
Good Answer 5 days ago, created an answer that was upvoted at least 5 times. For C: Error at the end of HT-seq Analysis and output.txt with 0 bytes in size
Scholar 5 days ago, created an answer that has been accepted. For A: logCPM to RPKM
Teacher 5 days ago, created an answer with at least 3 up-votes. For C: Error at the end of HT-seq Analysis and output.txt with 0 bytes in size
Scholar 5 days ago, created an answer that has been accepted. For A: logCPM to RPKM
Scholar 6 days ago, created an answer that has been accepted. For A: logCPM to RPKM
Commentator 7 days ago, created a comment with at least 3 up-votes. For C: Performing Anova Test For Ngs Time Series Datasets
Commentator 7 days ago, created a comment with at least 3 up-votes. For C: How To Extract Information From Fastq Pair End Files
Appreciated 7 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 7 days ago, created an answer with at least 3 up-votes. For C: Error at the end of HT-seq Analysis and output.txt with 0 bytes in size
Scholar 7 days ago, created an answer that has been accepted. For A: logCPM to RPKM
Good Answer 12 days ago, created an answer that was upvoted at least 5 times. For C: Error at the end of HT-seq Analysis and output.txt with 0 bytes in size
Scholar 15 days ago, created an answer that has been accepted. For A: logCPM to RPKM
Teacher 16 days ago, created an answer with at least 3 up-votes. For C: Error at the end of HT-seq Analysis and output.txt with 0 bytes in size
Good Answer 16 days ago, created an answer that was upvoted at least 5 times. For C: Error at the end of HT-seq Analysis and output.txt with 0 bytes in size
Appreciated 16 days ago, created a post with more than 5 votes. For Replace me: bioinformatician/post-doc at the DZNE (Bonn, Germany)
Appreciated 16 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 C: Error at the end of HT-seq Analysis and output.txt with 0 bytes in size
Scholar 18 days ago, created an answer that has been accepted. For A: logCPM to RPKM
Teacher 19 days ago, created an answer with at least 3 up-votes. For C: Error at the end of HT-seq Analysis and output.txt with 0 bytes in size

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