Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan87k
Reputation:
86,880
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
6 hours ago
Joined:
5 years, 10 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 • 9,790 results • page 2 of 979 • next >
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Comment: C: to get each covariate with PC loading in PCA
... So you want something like the following but with the length of each arrow indicated? ![enter image description here][1] [1]: https://i0.wp.com/2.bp.blogspot.com/-4ctMUwsp-Do/U7MBmncGYnI/AAAAAAAAAuE/J0y7Fyc7tvE/s1600/Scotch+Whiskies+Biplot.jpeg?resize=400%2C363 ...
written 6 days ago by Devon Ryan87k
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Comment: C: Hi-C: getting intervals from "A Compendium of Chromatin Contact Maps Reveal Sp
... Yeah, it appears that they didn't upload the most useful files. I've talked to folks internally and the consensus is that it's easiest to see if they can simply provide them. ...
written 6 days ago by Devon Ryan87k
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Comment: C: Hi-C: getting intervals from "A Compendium of Chromatin Contact Maps Reveal Sp
... Allegedly you can run `fit-hi-c` on these files to generate TAD calls. ...
written 6 days ago by Devon Ryan87k
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Comment: C: ChIp-seq RNA-seq overlap
... Yes, though it looks like you have an older version of deepTools, since I think I fixed the issue with the tick labels not being correct in more recent versions. ...
written 6 days ago by Devon Ryan87k
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Comment: C: to get each covariate with PC loading in PCA
... You're looking for "factor analysis", which is related to PCA but not exactly the same. ...
written 6 days ago by Devon Ryan87k
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Comment: C: Extracting data in a particular Format- only Raw counts in matrix format
... What have you tried? This looks like a job for `dplyr` in R (plus `cut` on the command line to make things quicker). BTW, I replaced "10 Lakhs" with "10 million", since a Lakh is a concept that doesn't exist outside of India. ...
written 6 days ago by Devon Ryan87k
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Comment: C: install Bioconductor package and its dependencies
... You can point rstudio to any R you want, so point it to the one from conda. ...
written 7 days ago by Devon Ryan87k
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Comment: C: install Bioconductor package and its dependencies
... Stop trying to compile things, use conda for EVERYTHING. ...
written 7 days ago by Devon Ryan87k
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Comment: C: ChIp-seq RNA-seq overlap
... They don't cover the whole plot because the two datasets are different size. In general using `--perGroup` with a dataset like that doesn't make sense, as the columns of data for each sample aren't comparable (only the rows are). ...
written 7 days ago by Devon Ryan87k
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Comment: C: install Bioconductor package and its dependencies
... Define "not working". ...
written 7 days ago by Devon Ryan87k

Latest awards to Devon Ryan

Good Answer 1 day ago, created an answer that was upvoted at least 5 times. For A: When should you use SVA vs. ComBat?
Good Answer 2 days ago, created an answer that was upvoted at least 5 times. For A: When should you use SVA vs. ComBat?
Appreciated 2 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Normalizing Rna-Seq Data Using Ercc Spike-In
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Normalizing Rna-Seq Data Using Ercc Spike-In
Scholar 5 days ago, created an answer that has been accepted. For A: Correlation analysis between gene expression & tumor purity
Good Answer 6 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 8 days ago, created an answer that has been accepted. For A: How To Create A Bigwig File And Display It
Scholar 9 days ago, created an answer that has been accepted. For A: How To Create A Bigwig File And Display It
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Normalizing Rna-Seq Data Using Ercc Spike-In
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: Where Is Mirna Binding Site On Mrna ?
Appreciated 4 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: When should you use SVA vs. ComBat?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Where Is Mirna Binding Site On Mrna ?
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Rna-Seq Library Design With Different Sequencing Depth
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Deseq Vs Edger..Filtering Read Counts.
Appreciated 5 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: Where Is Mirna Binding Site On Mrna ?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Where Is Mirna Binding Site On Mrna ?
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Bwa Mem Method For Mapping, With Or Without Trimming Reads?
Appreciated 7 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 7 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs

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