Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan97k
Reputation:
96,730
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
2 days, 10 hours ago
Joined:
7 years, 7 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 • 10,356 results • page 1 of 1036 • next >
4
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Answer: A: Scaling vs normalization in bamCompare
... Normalizing put values on a (somewhat) universally coherent value range. For example, `--normalizeUsing RPGC` will normalize the sample(s) to 1x coverage before proceeding. Scaling is done when you have 2 samples and needs to be done to make them comparable (i.e., it corrects for differences in sequ ...
written 2 days ago by Devon Ryan97k
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Answer: C: update salmon with conda
... Make sure conda-forge and bioconda are in your channels: `conda install -c conda-forge -c bioconda salmon=1.3.0`. I assume you're not running this on Windows, since we (Bioconda) only ship for Linux and OSX at the moment. ...
written 8 days ago by Devon Ryan97k
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Comment: C: Doubt on removing duplicates on amplicon sequencing data
... Depends on how badly affected they are, in general if the transcripts are highly enough expressed you're going to start having false-positive duplicates, so it's best to avoid that unless you really need to. ...
written 8 days ago by Devon Ryan97k
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Comment: C: deepTools computeMatrix need at least one array to concatenate error
... You have some sort of major name mismatch between the BED and bigWig files or there are simply no entries in the bigWig file within the regions specified by the BED file. ...
written 10 days ago by Devon Ryan97k
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Comment: C: Plot a dotted line to the start of the regions in computeMatrix, deepTools
... You might check if there's a newer version. I recall implementing this in one of the later 3.4 releases. Perhaps this got broken in 3.5, in which case please make a bug report. ...
written 18 days ago by Devon Ryan97k
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Comment: C: Comparing input read subtracted ChIP-read profiles using Deeptools v3.4.3
... Yes to all of the questions in your comment. ...
written 18 days ago by Devon Ryan97k
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Answer: A: Comparing input read subtracted ChIP-read profiles using Deeptools2
... You seem to be using deepTools 3.x rather than deepTools2. The guts of read count normalization is the following bit of code: mapped_reads = [bam1_mapped, bam2_mapped] # new scale_factors (relative to min of two bams) scale_factors = float(min(bam1_mapped, bam2_mapped)) / np.array(map ...
written 22 days ago by Devon Ryan97k
1
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Answer: A: Flip the heatmaps of ChIP-seq data to match TSS of +/- strand in deeptools
... Just include the strand in the normal position (column 6) and this will be done automatically by deepTools. ...
written 22 days ago by Devon Ryan97k
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Answer: A: Plot a dotted line to the start of the regions in computeMatrix, deepTools
... If you use `--referencePoint center` then you will get a dotted line on both ends (otherwise at least one end will be vertically aligned across genes, making such a guide line unnecessary). ...
written 22 days ago by Devon Ryan97k
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Comment: C: GTF/GFF file for feature count
... sed "s/''$//" foo.gtf > foo.fixed.gtf Note that the middle ticks are two apostrophes, not a ". Assuming you have EXACTLY the problem faced in the original post then that will fix it. ...
written 23 days ago by Devon Ryan97k

Latest awards to Devon Ryan

Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Comparing gene expression overlap with hypergeometric distribution
Scholar 2 days ago, created an answer that has been accepted. For A: Comparing gene expression overlap with hypergeometric distribution
Scholar 12 days ago, created an answer that has been accepted. For A: Comparing gene expression overlap with hypergeometric distribution
Appreciated 12 days ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Appreciated 14 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 A: Comparing gene expression overlap with hypergeometric distribution
Scholar 18 days ago, created an answer that has been accepted. For A: Comparing gene expression overlap with hypergeometric distribution
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: Comparing gene expression overlap with hypergeometric distribution
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: What statistical test for CpG DMR ?
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: R - pheatmap - changing column order
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: What statistical test for CpG DMR ?
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 7 weeks 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 7 weeks ago, created an answer that has been accepted. For C: What is "Possible polymerase run-on fragment"?
Scholar 7 weeks ago, created an answer that has been accepted. For A: Making a Model Matrix for Anova-like analysis
Good Answer 7 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.
Appreciated 7 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: R - pheatmap - changing column order
Good Answer 9 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 10 weeks ago, created an answer that has been accepted. For A: How to make it significant
Scholar 10 weeks ago, created an answer that has been accepted. For A: Making a Model Matrix for Anova-like analysis
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: Only doing log2 transformation for RNAseq read count data without normalizing by
Good Answer 10 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.
Teacher 11 weeks 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 11 weeks ago, created an answer that has been accepted. For A: Making a Model Matrix for Anova-like analysis

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