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bioinformatician.bsky.social
Senior Bioinformatics scientist at @mpipz_cologne. Previously postdoc at the @RaineyLab in @MPI_EvolBio. Data Science, Bioinformatics, Machine Learning, R, Rcpp, Python
29 posts 354 followers 107 following
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Here is a repository with the exercises I use in my data visualization class. We cover ggplot2/shiny and then consider different types of data (network, text, ...) and models (clustering, ...). I've tried to make the problems somewhat realistic. Feel free to reuse! github.com/krisrs1128/d...

submitted 25 days ago • 0 comments

Hello network #bioinformatics @tommytang.bsky.social Which are the best tools to take an AlphaFold model and extract: ➢ secondary structure types (helices, sheets) ➢ bond types (e.g. disulfide bonds) ➢ amino acids at critical positions ➢ possible subunits, function & cellular localization?

submitted 26 days ago • 2 comments

#TidyTuesday week 19: Seismic Events at Mount Vesuvius 🌋 A quick one looking at the relationship between depth and duration magnitude. #Rstats #dataviz #ggplot2

submitted 26 days ago • 2 comments

Do you like potatoes? Don't miss our most recent work on tetraploid potato genome! @nature.com #potato #genomics #history #evolution

submitted 54 days ago • 0 comments

Matchday 3️⃣2️⃣: #LFC 2️⃣-0️⃣ West Ham United Another step closer to the title 😅 #LIVWHU #rstats #ggplot2

submitted 61 days ago • 1 comment

This is my contribution for this week's #TidyTuesday 📊 I used the dataset provided and added the median household income per state — wondering if higher salaries would mean shorter emergency department wait times. Turns out, I was wrong 😅 #ggplot2 #RStats #DataViz #EmergencyCare

submitted 63 days ago • 2 comments

Here's my contribution to this week's hashtag#TidyTuesday. This time I worked with the Pokémon dataset — fitting, since Pokémon has been a big part of both my childhood and adulthood. #R #ggplot2 #TidyTuesday #RStats #DataViz #ggplot2 #Pokemon

submitted 75 days ago • 2 comments

ggpal2 dependencies have been updated to use "chores" (fka "pals")! 🗄️🧹📈

submitted 85 days ago • 2 comments

“In the current trials, we do a biopsy of the patient, sequence the tissue, send it to the pharmaceutical company, and they design a personalized vaccine that’s bespoke to that patient’s cancer. That vaccine is not suitable for anyone else. It’s like science fiction.”

submitted 90 days ago • 2 comments

🚨 Evolution Isn’t So Simple! 🚨 New research reveals that population structure can allow disadvantageous mutations to persist—challenging traditional evolutionary theory. 🧬🔬 📖 Read more: www.evolbio.mpg.de/3810220/news... #Evolution #Science #Genetics #Biology #Research

submitted 94 days ago • 0 comments

The 1st hour of "Interactive Visual Dashboards Using R Shiny" with Adam D. Rennhoff is now on YouTube! Get started with ggplot2 and the #tidyverse, then join us April 30-May 2 to learn how to build and deploy interactive dashboards with #RShiny in #Rstats.

submitted 100 days ago • 0 comments

www.science.org/doi/10.1126/.... The original paper Experimental Evolution of Evolvability by M. Barnett from Paul Rainey’s group, along with Edo Kussell’s story, are both fascinating. A brilliant example of experimental evolution at its finest.

submitted 101 days ago • 0 comments

🚀 New Study: Can evolution have foresight? 🧬🔬 A new study shows natural selection can shape genetic systems for future adaptation—challenging the idea that evolution is blind. Find out more: www.evolbio.mpg.de/3807853/news...

submitted 113 days ago • 0 comments

Animated Maps in R youtu.be/ra3BrCW5o54?... #rstats #ggplot2

submitted 108 days ago • 1 comment

Quantitative genetics is poorly understood by many biologists, and that's surely a failure in how it is taught. But teaching biology as 'fundamentally complex' seems like one of the least promising educational ideas since those 1970s schools that made lessons optional. www.cell.com/cell-systems...

submitted 111 days ago • 2 comments

My Tidyverse local synteny visualizer is up on GitHub: github.com/cxli233/Tidy... GitHub page contains 2 example datasets, as well as step-by-step instruction & explanations on how it works. Details on required input data are discussed in the GitHub page. Let me know if you run into issues.

submitted 184 days ago • 2 comments

For the "Working with Colors" 🎨 chapter of my book, I am also talking about good and bad color choices. Likely the most problematic color choice remains data encoded by the rainbow and jet colormaps. Here is a figure I am working on as an illustrative example plus some potential alternatives.

submitted 507 days ago • 2 comments

YES

submitted 210 days ago • 0 comments

Do you want to learn how to visualise your genomic data with R? Do not look any further! Check out our new course with @bioinformatician.bsky.social in November: physalia-courses.org/courses-work... #Genomics #DataViz #RStats

submitted 435 days ago • 0 comments

Dear friends, 🌋 𝐠𝐠𝐯𝐨𝐥𝐜 I'm excited to share some new features I've added to my 𝐠𝐠𝐯𝐨𝐥𝐜 R package for making volcano plots! 👩‍🔬 Have a look in here github.com/loukesio/ggv... and feel free to ⭐ the repo!

submitted 610 days ago • 2 comments

🚦Dear Blooskies, We have an updated version of our ltc package, which contains, among other enhancements, colour palettes based on the life and art of Pablo Picasso! Find it here: github.com/loukesio/ltc... 🎨🖌️

submitted 649 days ago • 0 comments

New work from my group, led by Michael Miller. In this paper, we assess the effectiveness of cooperation enforcement in Dictyostelium (social amoeba) www.biorxiv.org/content/10.1...

submitted 651 days ago • 2 comments

@mrebolleda.bsky.social and I are very excited to host the US West Hub of the MEEHubs24 conference (meehubs.org) in San Diego Jan 9-11, 2024. We have an outstanding lineup of speakers across all hubs! Registration is open until Sept 29. Please apply! It's free. #evolution #ecology

submitted 653 days ago • 0 comments

Publication alert! 🚨 Our work on identifying mobile elements in evolving compost communities is out in ISME communications! 🦠🧬 Link: rdcu.be/dkAsc Let me briefly summarise the paper in my first Bluesky thread:

submitted 655 days ago • 4 comments

Presenting bioinformatics pipelines visually takes time. I wish there was a flowchart tool to easily generate SVG diagrams! It takes me about an hour to make one manually. If anyone knows of a tool to streamline this, please share! I am sharing one in SVG in case it helps someone to save time!

submitted 657 days ago • 3 comments

Decided to post this here. It seems good that my first post is also the first preprint with an author from my lab! We used previously identified metabolic rules to predict microbial community assembly along a temperature gradient (1/12). www.biorxiv.org/content/10.1...

submitted 660 days ago • 1 comment

Dear blskyers, In collaboration with Kristian Ullrich, I'd like to present SNPless, a Nextflow pipeline developed for time series analysis of microbial genomics data 🧬. github.com/kullrich/snp...

submitted 659 days ago • 1 comment

🙀 Microsoft has integrated Python into Excel, which opens up powerful new capabilities. 🙀 😎 This means you can now leverage the full power of Python - including AI, ML, advanced calculations and more - directly within Excel spreadsheets. 📹 check the video, CRAZY www.youtube.com/watch?v=FbBX...

submitted 661 days ago • 1 comment