Samples returned from the asteroid Ryugu contain all five canonical nucleobases (A, G, C, T, U). Their presence in Ryugu and Bennu supports the hypothesis that carbonaceous asteroids contributed to the prebiotic chemical inventory of early Earth. http://dlvr.it/TRWtVp ☄️
Here is a short example of how to create a phylogenetic tree like the one on the left. I use data and silhouettes provided by the ggtree package — more is coming in the next days!
#ggtree #rstats #phylogenetics #dataviz #bioinformatics #ggplot2 #PhyloPic code: gist.github.com/loukesio/dd3...
thats a very interesting phylogenetic tree that reflect the avian evolution. I know its a big jump, but can we build something like this with #ggtree ?
www.nature.com/articles/s41...
Styling ggtree branches is easy; change color, linewidth, and linetype directly inside the ggtree() call. Works the same across rectangular, circular, and slanted layouts. Colors from the alger palette (ltc package).
#ggtree #rstats #phylogenetics #dataviz
thank you Trevor 😀!
More stuff related to #ggtree are coming
The cool things about ggtree don't stop here. You can use geom_text() or geom_label() to display node and tip labels simultaneously, or geom_tiplab() to show only tip labels. You can even have nodes and tips looking differently
#ggtree #rstats #phylogenetics #dataviz #bioinformatics #ggplot2
How to Design Antibodies
A step-by-step guide to making de novo binders. www.asimov.press/p/antibody-...
Nice to see this published at @PLoS Comp Bio. Big improvements after peer review and important input from @gsherloc.bsky.social! Hopefully, this tool will be helpful for those interested in using barcodes for detecting new beneficial mutations.
journals.plos.org/ploscompbiol...
Derived layouts build on top of those by flipping, rotating, or transforming coordinates — one extra line turns a rectangular tree into a dendrogram or an inward circular plot.
Base layouts (rectangular, slanted, circular, fan, daylight…) control the overall shape of the tree.
#ggtree has a relatively steep learning curve. But after looking at a few Python alternatives eg., toytree, ETE, Bio.Phylo it's hard to match its layout versatility. 21 tree variants with just a few lines of code.
#rstats #phylogenetics #bioinformatics
I would just love to have a simpler way to update RStudio less frequently on macOS, Windows, and Linux, or ideally have it happen with a single click. Indeed we can discuss it over an email.
Thank you, Dirk. My statement should in no way diminish the love for R or the outstanding work the community is doing I use it every day across multiple computers.
Definitely not the biggest problem in the world right now, but constantly installing new versions of RStudio, R and R packages is getting old fast. 😤 #RStats #DataScience
I hope you've found this post helpful.
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Study finds ChatGPT Health did not recommend a hospital visit when medically necessary in more than half of cases. www.theguardian.com/technology/2...
Want to master genomics data visualization with Python?
Join our online course with @bioinformatician.bsky.social (15–17 June ) and learn to create publication-quality plots—from volcano and Manhattan plots to phylogenetic trees—using top Python libraries.
www.physalia-courses.org/courses-work...
5/ How standard tools behave depends on depth.
DESeq2, edgeR, limma-voom with size-factor or TMM normalization handle moderate depth differences fine. But artifacts explode when depth is very low or tightly confounded with condition.
1. phantompeakqualtools still works github.com/kundajelab/...
2. I optimized ROSE for super-enhancer identification. now it finishes within 10mins! It was 12 hours! github.com/crazyhottom... now install via pip!
TSniffer: unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data link.springer.com/article/10....
Austria's newly famous tool-using cow - maybe it should have been a co-author? "Flexible use of a multi-purpose tool by a cow" - www.cell.com/current-biol...
Nature Genetics: Engineering AI co-scientists for statistical genetics applications www.nature.com/articles/s41... 🧬💻🧪 read free: rdcu.be/eZ2wR
All you want for christmas is.... transposon mutagenesis!
Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team.
Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)
A special shout-out to the amazing people who have shaped my approach to slide design and teaching, particularly Cédric Scherer, whose work continues to inspire how I think about making complex concepts accessible and visually engaging.
🔄 Stay tuned, we're constantly updating the materials and preparing for new adventures in genomics data visualization. 𝗠𝗼𝗿𝗲 𝗶𝗱𝗲𝗮𝘀, 𝗰𝗼𝘂𝗿𝘀𝗲𝘀, 𝗰𝘂𝘀𝘁𝗼𝗺 𝗽𝗮𝗰𝗸𝗮𝗴𝗲𝘀, 𝗮𝗻𝗱 𝗮 𝗯𝗼𝗼𝗸 𝗼𝗻 𝗴𝗲𝗻𝗼𝗺𝗶𝗰𝘀 𝗱𝗮𝘁𝗮 𝘃𝗶𝘀𝘂𝗮𝗹𝗶𝘇𝗮𝘁𝗶𝗼𝗻 𝗮𝗿𝗲 𝗰𝗼𝗺𝗶𝗻𝗴.
𝗢𝘂𝗿 𝗔𝗻𝗻𝘂𝗮𝗹 𝗚𝗲𝗻𝗼𝗺𝗶𝗰𝘀 𝗩𝗶𝘀𝘂𝗮𝗹𝗶𝘇𝗮𝘁𝗶𝗼𝗻 𝗖𝗼𝘂𝗿𝘀𝗲 𝘄𝗶𝘁𝗵 Physalia courses 𝗵𝗮𝘀 𝘄𝗿𝗮𝗽𝗽𝗲𝗱 𝘂𝗽! All course materials are available: 👉 lnkd.in/gTnfFewM You'll find all the code, slides, and resources I used to prepare the course from basic ggplot2 concepts to advanced genomic visualizations using R.
Our final course of the year is a wrap! 🎉
Huge thanks to @bioinformatician.bsky.social and to all the participants who joined us this week to level up their #Genomics #DataViz skills.
We can’t wait to see your beautiful figures making their way into papers, posters, and presentations!
💻 Discover all the latest features of Nextflow on Dec 11, , including the new Plugin Registry, workflow inputs & outputs, and static types.
Plus, don't miss the opportunity to ask the creator of Nextflow (@paoloditommaso.bsky.social) anything! 🌟
🌟 Register now: hubs.la/Q03W12B90
