Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan96k
Reputation:
95,900
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
2 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

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Comment: C: SizeFactors for BAM normalization
... No, there's no way to feed the file names in via a file, since we kind of assume that anyone handling that many files is using something like snakeMake to automatically generate the command. As an aside, it's tough to interpret any plots with that many samples. ...
written 2 hours ago by Devon Ryan96k
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Comment: C: SizeFactors for BAM normalization
... Correct, you don't need to account for library size. ...
written 1 day ago by Devon Ryan96k
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Answer: A: Limma:Coefficients not estimable, please help
... You can't estimate placebo effect AND treatment effect, since one is the reverse of the other (i.e., placebo is necesarily the opposite of treatment). Likewise, estimating the effects of male and female makes no sense, since you need some baseline for comparison (i.e., if you measure the effect of b ...
written 1 day ago by Devon Ryan96k
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Answer: A: SizeFactors for BAM normalization
... Please use `1/calcNormFactors(object = raw.count)` as the scaling factor. Whether you use TMM or the default RLE is largely immaterial to me. Your `bamCoverage` command looks fine. ...
written 1 day ago by Devon Ryan96k
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Comment: C: RNA SEQ VS CHIP SEQ....
... Good bye, you are undeserving of help. Your account is now suspended and it will not be reactivated. ...
written 1 day ago by Devon Ryan96k
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Comment: C: TSS metaprofile using Deeptools
... If you want genes then that will work fine. Just remember that genes are just groups of transcripts when looking at the results. ...
written 5 days ago by Devon Ryan96k
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Comment: C: cram file to fastq conversion
... Sounds like the chromosome names don't match or they're in a different order. Compare the header from the CRAM file to the chromosome names in the fasta. ...
written 6 days ago by Devon Ryan96k
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Comment: C: Deeptools ValueError: invalid literal for int() with base 10 error
... Yup, exactly ...
written 6 days ago by Devon Ryan96k
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Comment: C: Deeptools ValueError: invalid literal for int() with base 10 error
... Can you `grep e` on your BED file? ...
written 6 days ago by Devon Ryan96k
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Comment: C: Deeptools ValueError: invalid literal for int() with base 10 error
... Can you post the command you used and the entire error message? Do you have a position in your BED file of literally 3.2e+07? ...
written 6 days ago by Devon Ryan96k

Latest awards to Devon Ryan

Appreciated 1 day ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 1 day 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 1 day ago, created an answer that has been accepted. For A: Making a Model Matrix for Anova-like analysis
Teacher 5 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 5 days ago, created an answer that has been accepted. For A: Making a Model Matrix for Anova-like analysis
Good Answer 5 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 13 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 13 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 13 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 15 days ago, created an answer that was upvoted at least 5 times. For A: R - pheatmap - changing column order
Good Answer 15 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 15 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 28 days ago, created an answer with at least 3 up-votes. For A: filtering paired end mapped reads form SAM/BAM file
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Making a Model Matrix for Anova-like analysis
Scholar 28 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

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