If you'd like your files to be ordered by "last modified" in the explorer, you can append the following config to your settings.json: { "explorer.sortOrder": "modified" } Works both in #positron and in #vscode.

If you are using independent training and testing sets which need PCA calculation in genomics, be sure to do it using projection and to the same panel, alongside the same parameters (maf, ld and missingness). Otherwise, you are comparing bananas to apples. #genomics #bioinformatics

Speak at posit::conf(2026) and share your R & Python stories! Accepted speakers get: ✨ Travel & lodging help ✨ Free conference pass ✨ Professional coaching Apply by Feb 6 to join us Sept 14-16 in Houston, TX! Submit here: pos.it/conf-talk-2026 #positconf2026 #rstats #pydata

3 things I learned from @stephenturner.us workshop on #R pkg development in #Positron - there is a light bulb icon that creates a roxygen template for an R file - available::available("pkgname") checks if the name you want has already been used - {pkgndep} evaluates heaviness of pkg dependencies

I use a gist everytime I need to run a few basic #bioinformatics explorations in a new instance, and thought I could share it here so someone could benefit from it too! I have forked it and adapted a bit to my needs. Here it goes: gist.github.com/flaviaerius/...

I won't miss this one!

poisonfrogs: Color Palettes Inspired by Neotropical Poison Frogs laurenoconnelllab.github.io/poisonfrogs/ #Rstats

Really nice work by @nbaya.bsky.social and co. showing that, as expected, individuals whose observed phenotype deviates from their genetically predicted trait are enriched for rare damaging variants in associated genes with said trait. Now to see if embryo selection companies pick up on this 😉

Crazy interesting biology! I wonder if there is any phenotypic evidence of this chimerism.

#RStats Friends, for those of you who need to work with #RStudio in Windows I've put a survival guide for you here. github.com/eriksquires/...

Turn YAML into R and R into YAML with the new {yaml12} #RStats 📦 posit-dev.github.io/r-yaml12/ind... By @t-kalinowski.bsky.social On the 📦 website: "YAML in 2 Minutes: A Gentle Introduction for R Users" posit-dev.github.io/r-yaml12/art...

polars-bio—fast, scalable and out-of-core operations on large genomic interval datasets academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/biodatageeks...

Tech I'm thankful for blog.stephenturner.us/p/tech-im-th... #rstats 🧬🖥️🧪

Tip for formatting text on Google Docs by Gemini *without changing content*: If the text is in one language, use the prompt to format in another language. It worked perfectly for me! Before that, every time I asked it to "format without changing text" it failed. #gemini

My talk on #positconf2025 is available on Youtube! Check it out: youtu.be/phh8p2ImBMQ?...

🧬 PRSs in practice (3/5): Higher-risk results = behaviour change? A common concern is that higher-risk polygenic risk scores (PRSs) don’t motivate lifestyle behaviour change. My @nathumbehav.nature.com paper with @mikeinouye.bsky.social addresses this 👉 rdcu.be/eNeKN #Genomics #BehaviourChange

So interesting! Highest SNP heritabilities (which mean variation explained by genetics) after controlling for parent education and birthplace were around 10% for social sciences and journalism, for arts and humanities, and for natural sciences, mathematics and statistics.

About PRSs in the clinics: people do not understand risk in general, not only the risk related to PRS. The solution is educating health professionals to communicate PRS risk (and other risks) clearly.

4 word horror story for an R user: "has a Java dependency"

Probably late, but his week I finally understood the meaning of prompt engineering. I used a prompt, extracted results, measured them, then adjusted both the input and prompt for better results, measured them, adjusted inputs again, measured results, and finally applied to a new dataset.

Ever wondered why analyzing RNA-seq data feels like walking through a fog with 20,000 dimensions? Let’s talk about the curse of dimensionality in bioinformatics—and why it’s not just a math problem, it’s a biological one. 🧵

I just want to share that I had a blast at #positconf2025! Met so many wonderful people, and gave a talk for the first time. It was awesome!

I’m new to bluesky,so.. hi! I’m Beatriz / Bea, from Brasil, and currently I’am a post doc researcher. I started to learn how to program in R in 2018 to use it on my research, and have been programming since then. I have a blog where I post and share presentations etc beamilz.com #rstats 👋

I have just experienced the magic of rv in recovering my R packages after having to format my laptop. Completely recommend! github.com/A2-ai/rv #rstats

Every #Rstats user should read this post from @jennybryan.bsky.social‬. Especially beginner to intermediate-level ones. www.tidyverse.org/blog/2017/12...

My biggest, loudest job application advice: WHY do you want this job? This SPECIFIC job? What about it interests you? What do you think of it? What can you bring to it? I know this sounds obvious but a generic cover letter isn't doing you favours - really. *Show me you know the job!* 1/7

TIL you can set different values of alpha based on categories on #ggplot2. Set 'aes(alpha = categories_col)', and then use scale_alpha_manual() to set specific transparency proportions. I used a lower alpha in order to visualize the most important categories here. #rstats

1/ When should you use a package vs. solving from scratch in bioinformatics? I get asked this all the time. Here’s my approach: 👇

TIL the parameter .before in mutate() from {dplyr}. It adds the new column(s) created to the *beginning* of the dataframe, instead of to the end. Quite useful! Source: #RforDataScience (2e) (sometimes you should read stuff you think you already know) #rstats

“The idea that taking walks, reading things unrelated to your research, and hanging out with strangers in a campus pub should be considered part of the serious process of thinking, but might well meet with skepticism in practice.” www.pnas.org/doi/10.1073/...

Use "export" + the variable name and value when creating a chain of bash scripts, for it to be available in the called script too. For example: export LD_CORRELATION=0.2 bash run_ld_correlation_reference.sh bash run_ld_correlation_samples.sh #bioinformatics

I think prenatal genetic testing should become part of IVF. The cost of even a single embryo mix up is enormous. NIPT (for parental relatedness) is affordable and can be done early during pregnancy. Parents must have assurance about their child. thenightly.com.au/australia/mo...

Quick #bioinformatics tip: If you'll use plink files in your pipeline, whenever possible, transform your VCF into pgen or bgen ASAP! Plink files are much faster to work with.

I need to say that Lonely Planet is still better than chatGPT to find interesting attractions for a trip.

jq is so useful.

I have the impression, when reading papers from the 1990's and before, that concepts were explained more clearly than nowadays.

I have just used #Gemini 2.5 Flash as a reviewer for my Quarto doc, and it gave me interesting recommendations. My prompt asked for both text and #Rstats code reviews. It returned strong points and improvement suggestions. Useful tool especially for academics.

Today I went to the weekly seminar of the department I do my postdoc in (FMUSP), mostly remotely. It was great to interact with other researchers in-person. I miss this sometimes.

This workshop is tomorrow, don't miss your last chance to register! Details: bit.ly/3wBeY4S Please share! #AcademicSky #EconSky #Python

To clarify my poor post, it is NOT present in base R. Only when loading {data.table}. Still exciting for me, though! #rstats

YIL that %notin% is already a thing in R. I know it's been out for a while, from {data.table}, but I have discovered it yesterday. Yes, I was still using the structure !(column %in% vector). 🫠 Sharing in case you've missed it too! #rstats

Now that we know Brazil has one of the most admixed populations in the world, make sure to have a look on our recently published paper on the validation of two #BreastCancer #PRS in a large cohort of Brazilians (N=15k)! doi.org/10.3390/diag...

If you haven't registered yet, this is your last chance! Come with me to learn how to extract and clean tables from PDFs using #RStats, and help Ukraine at the same time!

Are you interested in learning how to extract tables from PDFs using simple and effective R tools? I’ll give a workshop next week as part of the Workshops for Ukraine initiative. More details and registration here: sites.google.com/view/dariia-... #rstats

On May 1st we will have a workshop on how to convert PDF tables to usable data with R by @flaviaerius.bsky.social More info: bit.ly/3EvUQZQ #EconSky #AcademicSky #RStats

🦤 The first de-extinct animal has just been born! @ucsantacruz.bsky.social 's Beth Shapiro is part of the team that made it happen. Watch Shapiro and her colleagues at Colossal explain the de-extinction of the Dire Wolf: www.youtube.com/watch?v=F5uC...

I was teaching some #rstats at work and I forget about all the entry level challenges that can turn off newcomers to learning coding. In these case it was file path convention between windows and linux three things that really help are: 1) {here} package 2) base::normalizePath 3)base::file.path

The most efficient tips for working with a large dataset are: 1. Subset your data to small chunks If your computer crashes, keep subsetting, until it doesn't. 2. Use command line and a plain text editor Forget positron, Rstudio or VScode. They are too heavy. #bigdata #rstats

Are you getting into the #bioinformatics area coming from a #biological sciences background? This new blog post is for you! How To Operate Large Files in Bioinformatics Definitely my past self would have benefited from it. Enjoy! flaviaerius.com/posts/big-da...