An American in Germany, an ion channel guy in bioinformatics, a proponent of scientific skepticism in an irrational world. @devon@genomic.social
Freiburg, Germany
Joined January 2010
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Devon Ryan retweeted
Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic ... biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
Glad they learned their lesson there. Did anyone like 0/0 for no calls?
GATK 4.6.0.0 reverts back to ./. for no-calls instead of 0/0 with DP=0 github.com/broadinstitute/ga…
Devon Ryan retweeted
SeqKit is an absolutely amazing tool! I was writing a custom script to chunk reorder the records in a large reference file, and then chunk them into sub-files of a pre-specified size. The script wasn't huge, but was slow & error prone. Alternatively; it's just 2 seqkit commands!
SeqKit2: A Swiss army knife for sequence and alignment processing. It suit for nanopore data! #nanopore doi.org/10.1002/imt2.191
Devon Ryan retweeted
Minimap2-2.27 released with new presets for accurate Nanopore reads and Illumina Complete Long Reads (both recommended by vendors), along with a few minor features and bug fixes. Output alignment identical to v2.26 except the value at a custom tag. github.com/lh3/minimap2/rele…
Devon Ryan retweeted
Very happy to see simpleaf published! @DongzeHe and I are working on some exciting improvements and expansions that I'm looking forward to sharing more about soon :).
simpleaf : A simple, flexible, and scalable framework for single-cell data processing using alevin-fry. #SingleCell #DataProcessing #Rust #Bioinformatics @nomad421
academic.oup.com/bioinformat…
Devon Ryan retweeted
Do you use pysam? Currently #pysam builds wheels back to Python 3.6, which has been end-of-life for a couple of years. Please let us know via this survey which Python versions you use and would like pysam to continue supporting. github.com/pysam-developers/…
Gotta say I'm feeling this at the moment. The downside to making conda packages out of anything that could prove useful is that I end up looking at the code and... yeah... well, what Nils said.
Devon Ryan retweeted
#Genedata collaborates with @AstellasPharma to help confirm the #biosafety of cell therapies using #NGS-based assays within a validated environment. Read more at buff.ly/45XzA7Z
#DigitalizingBiopharma #GenedataSelector #Bioinformatics #gmp #Celltherapy
Devon Ryan retweeted
And finally, it is great to have more than one freely available and well suitable tool to get the job done. What matters is that science is reproducible and transparent, and that these properties are strived for as many people as possible. (3/x)
I've said it before and I'll say it again, it's important that you use A workflow manager, not really which one you use. It's vital to get familiar enough with one to be productive and make reproducible and redistributable analyses. The exact choice is then totally "you do you".
TIL that a pie chart is referred to as a Camembert in French and I think we should absolutely call it this in English now!
After a pause over the weekend (because I seem to have broken Anaconda's CDN sync) this is now up and running again. ~700 packages down, ~2300 to go.
Devon Ryan retweeted
Clustering algorithms report clusters even when none exist. In single-cell RNA-Seq pipelines, novel cell types are often identified by clustering algorithms. Expanding on Kimes et al.'s work, we introduce significance analysis for single-cell RNA-Seq data: nature.com/articles/s41592-0…
Devon Ryan retweeted
bedder-tools 😜 is the next generation of bedtools from @aaronquinlan lab. It's early days, but we think the foundation is solid. We're looking for feedback on the rust code. Have a look: github.com/quinlan-lab/bedde… and specifically about design here: github.com/quinlan-lab/bedde…
Devon Ryan retweeted
Pangene is a new tool for constructing a pangenome gene graph from multiple assemblies: github.com/lh3/pangene. You can explore the rich haplotypic diversity of human genes at pangene.liheng.org. Still WIP.
