Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan94k
Reputation:
94,390
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Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
Scholar ID:
Google Scholar Page
Last seen:
18 hours ago
Joined:
7 years 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: bedGraphToBigWig file converter
... Cross-posted on the bioinfo stackexchange: https://bioinformatics.stackexchange.com/questions/12836/bedgraphtobigwig-file-conversion ...
written 2 days ago by Devon Ryan94k
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Answer: C: Snakemake - Missing MissingInputException in line 20: Missing input files for ru
... I think the `tname` line should just be removed (and then remove the comma on the line above). ...
written 5 days ago by Devon Ryan94k
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Comment: C: Only doing log2 transformation for RNAseq read count data without normalizing by
... Normalization is not transformation, its purpose is not to make the data (more or less) normally distributed. Of the common RNA-seq packages, only voom results in a transformation to a normalish distribution, the others keep the data as is and use normalization to compute per-sample offsets for thei ...
written 6 days ago by Devon Ryan94k
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Comment: C: Snakemake SyntaxError: No rule keywords allowed after run/shell/script/wrapper/c
... My only guess is that there's a single space missing somewhere, since otherwise everything looks fine to me. ...
written 8 days ago by Devon Ryan94k
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Comment: C: Snakemake SyntaxError: No rule keywords allowed after run/shell/script/wrapper/c
... What comes after the `shell:` line? Most likely you have an indentation problem later, since what you posted looks fine. ...
written 8 days ago by Devon Ryan94k
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Comment: C: Software testing process failure: How can I match the already installed programs
... You may have installed TEPID via conda, but the one you installed via pip is what's actually getting used. Please do the following: PYTHONNOUSERSITE=True tepid-discover The "PYTHONNOUSERSITE" part will prevent python for looking at anything under `/home/silviav/.local`. ...
written 10 days ago by Devon Ryan94k
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Comment: C: Normalization of ATAC SEQ data for the proper deeptools heatmap
... I think whether you can normalize so peaks are most similar or background is most similar will depend a bit on the experiment. I've worked with a lot of people perturbing things in ways that I expect a large change in peaks. Given that normalizing for similar backgrounds make the most sense. If, how ...
written 24 days ago by Devon Ryan94k
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Answer: A: Normalization of ATAC SEQ data for the proper deeptools heatmap
... I wouldn't expect the peak heights to be identical, some amount of biological variation is normal. The goal of the normalization should instead be to set the background level to roughly similar values between samples. You do not need to normalize your BAM files, CSAW or DiffBind will take care of t ...
written 25 days ago by Devon Ryan94k
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Answer: A: legal issues about running the analysis on the cloud
... Whether it's legal or not depends on the contract you make with your cloud provider surrounding data access. The larger providers like AWS and Google cloud generally are already aware of privacy concerns and have legal agreements in place to meet compliance standards. But there will be country and p ...
written 26 days ago by Devon Ryan94k
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Answer: A: What is the difference between bed files from bigWig or bam, and bed files of na
... bigWig files are generally whole-genome coverage tracks, so you would need to call peaks on them. You can convert them to bedGraph format and then input that into MACS2 `bdgpeakcall`. Note however that you may have to manually play around with the parameters quite a bit to get reasonable peak calls ...
written 26 days ago by Devon Ryan94k

Latest awards to Devon Ryan

Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Making a Model Matrix for Anova-like analysis
Popular Question 5 days ago, created a question with more than 1,000 views. For Bioinformatician, DEEP consortium (Freiburg, Germany)
Appreciated 6 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 A: How To Find The Closest Distance From Bed Files Between Genes And Repeats That A
Scholar 13 days ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: How To Find The Closest Distance From Bed Files Between Genes And Repeats That A
Scholar 19 days ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Epic Question 24 days ago, created a question with more than 10,000 views. For Is There A Faster Replacement For Fastq-Dump (From The Sra-Toolkit)?
Scholar 25 days ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Scholar 26 days ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: Script To Calculate Length Distribution Of A Collapsed Fasta File
Scholar 4 weeks ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Rna-Seq: Novel Transcripts Found. What Next?
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Script To Calculate Length Distribution Of A Collapsed Fasta File
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Script To Calculate Length Distribution Of A Collapsed Fasta File
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Appreciated 5 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Scholar 7 weeks ago, created an answer that has been accepted. For A: How to obtain gene symbols from the result list of GEO2R?
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: Mapping God Found ‘Scientifically Dishonest’ By Anonymous Peer Reviewers
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: Rna-Seq: Novel Transcripts Found. What Next?
Appreciated 8 weeks ago, created a post with more than 5 votes. For BWA 0.7.11 is out, supports ALT contigs
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Script To Calculate Length Distribution Of A Collapsed Fasta File

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