Joined January 2010
- Tweets 2,335
- Following 180
- Followers 1,199
- Likes 2,937
44 Photos and videos
Devon Ryan retweeted
2 Dec 2024
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
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11 Jul 2024
Glad they learned their lesson there. Did anyone like 0/0 for no calls?
11 Jul 2024
GATK 4.6.0.0 reverts back to ./. for no-calls instead of 0/0 with DP=0 github.com/broadinstitute/ga…
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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!
7 Jul 2024
SeqKit2: A Swiss army knife for sequence and alignment processing. It suit for nanopore data! #nanopore doi.org/10.1002/imt2.191
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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…
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25 Oct 2023
I have 3 invite codes to the site where the sky is blue. Let me know if you want one.
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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 :).
14 Oct 2023
simpleaf : A simple, flexible, and scalable framework for single-cell data processing using alevin-fry. #SingleCell #DataProcessing #Rust #Bioinformatics @nomad421
academic.oup.com/bioinformat…
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Devon Ryan retweeted
8 Oct 2023
I got featured in the Fall 2023 edition of the Harvard Public Health Magazine!
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Devon Ryan retweeted
3 Oct 2023
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/…
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23 Sep 2023
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.
17 Sep 2023
Dear academics, I'm going to eventually read your code. Please feel the appropriate amount of shame from the start about your hard-coded paths, missing required files, and major assumptions about file naming. Your frenemy, industry.
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#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
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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)
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15 Sep 2023
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".
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16 Aug 2023
I see tweetdeck is now disabled for us normies. Nothing like making this site even less functional.
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8 Aug 2023
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!
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7 Jul 2023
FYI, the 3.17 Bioconductor packages are now getting pushed out to Bioconda.
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10 Jul 2023
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.
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20 Jul 2023
FYI, the should mostly all be there now. There are a couple dozen that need a bit more TLC or are waiting for some stragglers from the migration on conda-forge but 99% is there.
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Devon Ryan retweeted
10 Jul 2023
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…
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Devon Ryan retweeted
10 Jul 2023
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…
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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.
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