Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan98k
Reputation:
97,560
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
4 days, 5 hours ago
Joined:
7 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 • 10,372 results • page 1 of 1038 • next >
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Comment: C: hisat2 alignment error
... Looks quite malformed, you'll want to contact who ever uploaded it. ...
written 15 days ago by Devon Ryan98k
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Answer: A: ATAC-seq +4 -5 shift
... The shifting isn't for any real purpose unless you want to plot the exact cut location (e.g., when searching for motifs), it simply harkens back to one of the first ATAC-seq papers where they performed this adjustment to account for the 9-base single-stranded over-hang on each end of the fragment. P ...
written 15 days ago by Devon Ryan98k
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Comment: C: Extracting Methylation Data
... Your life will be much easier if you just install it with conda. ...
written 4 weeks ago by Devon Ryan98k
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Answer: C: Counting data with ht seq
... 1. If you want to use python, your life will be much easier if you use pandas to make data frames out of this. 2. You're going to use R in the next step anyway, so why not read it in (using DESeq2) with DESeqDatasetFromHTSeqCount and then: . KEEP = which(apply(counts(dds), 1, min) >= 5) ...
written 4 weeks ago by Devon Ryan98k
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Answer: A: Is it normal to obtain a perfectly dark blue "Per tile sequence quality" plot in
... Yes, that's common and not an issue ...
written 5 weeks ago by Devon Ryan98k
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Comment: C: Is there a stagewise testing procedure for DESeq2?
... If you figure out the steps feel encouraged to post a tutorial with that. I'm sure it'd be quite useful for many folks :) ...
written 7 weeks ago by Devon Ryan98k
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Comment: C: Is there a stagewise testing procedure for DESeq2?
... Wouldn't the [stageR](https://bioconductor.org/packages/release/bioc/vignettes/stageR/inst/doc/stageRVignette.html) package enable this for all possible upstream packages (e.g., DESeq2 and edgeR)? They use edgeR in their vignette because one of the authors wrote it, but there's no reason you couldn' ...
written 7 weeks ago by Devon Ryan98k
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Comment: C: How to count the number of codons in a frame or order using the equation?
... Further help comes at a cost of 500 euro per hour (or fraction thereof). I imagine you'll want to code the last bit yourself... ...
written 7 weeks ago by Devon Ryan98k
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Comment: C: RNAseq bad PCA, a differential expression analysis killer ?
... Inter-group variation should have been "intra-group variation", which is the same as experimental noise. At the end of the day the reason for no clustering is because the experimental variation dwarfs the effect size. So there's really nothing worth looking at in that regard. You just won't get a hu ...
written 7 weeks ago by Devon Ryan98k
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Answer: A: Converting to decimal values
... $ awk '{split($5, v, "/"); OFS="\t"; print $1,$2,$3,v[1]/v[2]}' foo.txt A B 2.9711e-01 0.000976562 A C 2.3343e-03 0.908691 A D 2.9711e-01 0.000976562 A E 2.9711e-01 0.000976562 ...
written 7 weeks ago by Devon Ryan98k

Latest awards to Devon Ryan

Teacher 11 days ago, created an answer with at least 3 up-votes. For A: Bwa Run With Fastq File With Different Read Length
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: Bwa Run With Fastq File With Different Read Length
Commentator 27 days ago, created a comment with at least 3 up-votes. For C: Perl Script To Make Statistics Of Mirna Abundances For Many Samples
Good Answer 27 days ago, created an answer that was upvoted at least 5 times. For A: Rna-Seq: Novel Transcripts Found. What Next?
Good Answer 4 weeks 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.
Scholar 5 weeks ago, created an answer that has been accepted. For A: Comparing gene expression overlap with hypergeometric distribution
Appreciated 5 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Perl Script To Make Statistics Of Mirna Abundances For Many Samples
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Bwa Run With Fastq File With Different Read Length
Appreciated 7 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 8 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 9 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 11 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Comparing gene expression overlap with hypergeometric distribution
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: A Quick Way To View Or Check The Order Of Chromosome In Bam File
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Comparing gene expression overlap with hypergeometric distribution
Scholar 12 weeks ago, created an answer that has been accepted. For A: Comparing gene expression overlap with hypergeometric distribution
Scholar 3 months ago, created an answer that has been accepted. For A: Comparing gene expression overlap with hypergeometric distribution
Appreciated 3 months ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 3 months ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Comparing gene expression overlap with hypergeometric distribution
Scholar 3 months ago, created an answer that has been accepted. For A: Comparing gene expression overlap with hypergeometric distribution
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Comparing gene expression overlap with hypergeometric distribution
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What statistical test for CpG DMR ?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: R - pheatmap - changing column order

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