Admin: Devon Ryan

gravatar for Devon Ryan
Devon Ryan80k
Reputation:
80,440
Status:
Trusted
Location:
Freiburg, Germany
Twitter:
dpryan79
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Google Scholar Page
Last seen:
an hour ago
Joined:
5 years, 3 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 • 9,249 results • page 1 of 925 • next >
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Comment: C: Is it correct if we use htseq counts as raw read counts in DESEq2?
... In this context, "raw counts" refers to unnormalized integer-only counts of reads/fragments uniquely mapping to genes. ...
written 1 hour ago by Devon Ryan80k
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Answer: A: Is it correct if we use htseq counts as raw read counts in DESEq2?
... Yes, the count files produced by htseq-count are appropriate input into DESeq2. BTW, featureCounts is much faster. ...
written 1 hour ago by Devon Ryan80k
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Answer: A: Best Software for analysis of Hi-C data
... I'll give the somewhat biased recommendation to try [HiCExplorer](https://github.com/deeptools/HiCExplorer). It will enable starting with fastq files and proceeding through heatmaps and further analysis. ...
written 21 hours ago by Devon Ryan80k
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Comment: C: The best way to produce gene body coverage
... As in a plot of it or a metric? ...
written 22 hours ago by Devon Ryan80k
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Answer: A: GATK3 error message
... Yes, your fasta file is likely corrupted, since it has a `\` in it as a base. ...
written 23 hours ago by Devon Ryan80k
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Comment: C: Sequence Length Distribution after trimmomatic
... I've moved this to an answer, since it's absolutely correct. ...
written 23 hours ago by Devon Ryan80k
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Answer: A: Batch and combining reads from two flow cells for the same ChIP/ATAC-seq library
... As a general principal, if you just sequenced the same library twice then go ahead and merge the results (it doesn't much matter if you `cat` the fastq files together or use `samtools merge` on the BAM files, you'll get essentially the same results regardless). In your particular case you've also n ...
written 1 day ago by Devon Ryan80k
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Answer: A: What is the difference between single-cell RNA-Seq and typical RNA-Seq in terms
... The main difference between scRNA-seq and standard RNA-seq is (A) a bit more complicated analysis workflow and (B) often different goals. The additions to the normal analysis in scRNA-seq include handling cell and UMI barcodes throughout the process so you can reach a reliable matrix of values per- ...
written 1 day ago by Devon Ryan80k
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Comment: C: qPCR: Huge variation in fold change of genes between biological replicates
... It sounds like you have variable degradation of your samples. ...
written 1 day ago by Devon Ryan80k
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Comment: C: EdgeR generic design matrix
... Yup, that'd be the equivalent. ...
written 1 day ago by Devon Ryan80k

Latest awards to Devon Ryan

Teacher 20 hours ago, created an answer with at least 3 up-votes. For A: Microarray Probesets Quality Control - Why exclude non-autosomal probesets?
Good Answer 1 day ago, created an answer that was upvoted at least 5 times. For A: How To Download The Entire Human Gene List With Their Chromosomal Location
Commentator 3 days ago, created a comment with at least 3 up-votes. For C: Performing Anova Test For Ngs Time Series Datasets
Good Answer 5 days ago, created an answer that was upvoted at least 5 times. For A: How To Download The Entire Human Gene List With Their Chromosomal Location
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Microarray Probesets Quality Control - Why exclude non-autosomal probesets?
Scholar 6 days ago, created an answer that has been accepted. For A: Microarray Probesets Quality Control - Why exclude non-autosomal probesets?
Scholar 6 days ago, created an answer that has been accepted. For A: Microarray Probesets Quality Control - Why exclude non-autosomal probesets?
Popular Question 6 days ago, created a question with more than 1,000 views. For BWA 0.7.11 is out, supports ALT contigs
Scholar 6 days ago, created an answer that has been accepted. For A: Microarray Probesets Quality Control - Why exclude non-autosomal probesets?
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Microarray Probesets Quality Control - Why exclude non-autosomal probesets?
Scholar 7 days ago, created an answer that has been accepted. For A: Microarray Probesets Quality Control - Why exclude non-autosomal probesets?
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Microarray Probesets Quality Control - Why exclude non-autosomal probesets?
Good Answer 9 days ago, created an answer that was upvoted at least 5 times. For A: How To Download The Entire Human Gene List With Their Chromosomal Location
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Microarray Probesets Quality Control - Why exclude non-autosomal probesets?
Scholar 10 days ago, created an answer that has been accepted. For A: Microarray Probesets Quality Control - Why exclude non-autosomal probesets?
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: how to get Homo_sapiens.GRCh38.84.bed file
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Concatenate Two .Fasta Files Into One
Scholar 12 days ago, created an answer that has been accepted. For A: how to get Homo_sapiens.GRCh38.84.bed file
Scholar 13 days ago, created an answer that has been accepted. For A: how to get Homo_sapiens.GRCh38.84.bed file
Scholar 13 days ago, created an answer that has been accepted. For A: how to get Homo_sapiens.GRCh38.84.bed file
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Concatenate Two .Fasta Files Into One
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Concatenate Two .Fasta Files Into One
Scholar 14 days ago, created an answer that has been accepted. For A: how to get Homo_sapiens.GRCh38.84.bed file
Scholar 14 days ago, created an answer that has been accepted. For A: how to get Homo_sapiens.GRCh38.84.bed file
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Concatenate Two .Fasta Files Into One

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