Flávia E. Rius
@flaviaerius.bsky.social
I work with Polygenic Risk Scores for Brazilians @ Mendelics
#rstats #bioinformatics
#rstats #bioinformatics
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
#genomics #bioinformatics
January 16, 2026 at 12:09 PM
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
#genomics #bioinformatics
Reposted by Flávia E. Rius
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
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
January 15, 2026 at 3:40 PM
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
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
- 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
January 15, 2026 at 11:55 PM
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
- 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 have forked it and adapted a bit to my needs. Here it goes:
gist.github.com/flaviaerius/...
Install samtools, bcftools and htslib on linux
Install samtools, bcftools and htslib on linux. GitHub Gist: instantly share code, notes, and snippets.
gist.github.com
January 12, 2026 at 1:12 PM
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 have forked it and adapted a bit to my needs. Here it goes:
gist.github.com/flaviaerius/...
I won't miss this one!
❗️Our next workshop will be on Jan 15 , 6 pm CET titled R package development in Positron by
@stephenturner.us
Register or sponsor a student by donating to support Ukraine!
Details: bit.ly/3wBeY4S
Please share!
#AcademicSky #EconSky #RStats
@stephenturner.us
Register or sponsor a student by donating to support Ukraine!
Details: bit.ly/3wBeY4S
Please share!
#AcademicSky #EconSky #RStats
January 9, 2026 at 3:55 PM
I won't miss this one!
Reposted by Flávia E. Rius
poisonfrogs: Color Palettes Inspired by Neotropical Poison Frogs laurenoconnelllab.github.io/poisonfrogs/ #Rstats
January 7, 2026 at 3:00 PM
poisonfrogs: Color Palettes Inspired by Neotropical Poison Frogs laurenoconnelllab.github.io/poisonfrogs/ #Rstats
Reposted by Flávia E. Rius
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 😉
Now to see if embryo selection companies pick up on this 😉
Why do some individuals defy their polygenic score?
In the largest study of its kind (402k UKB individuals; 7 continuous traits + 3 diseases), we asked: If your phenotype deviates from common-variant polygenic score prediction, what's driving that difference?
www.medrxiv.org/content/10.6...
In the largest study of its kind (402k UKB individuals; 7 continuous traits + 3 diseases), we asked: If your phenotype deviates from common-variant polygenic score prediction, what's driving that difference?
www.medrxiv.org/content/10.6...
January 7, 2026 at 5:46 AM
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 😉
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.
I wonder if there is any phenotypic evidence of this chimerism.
A fascinating case report.
The DNA of a female murder victim was genotyped and it turns out that she has been a chimera: a mixture of 46XX/46XY cell lines.
The analysis (STR-based) found:
1. The maternal chromosome was identical between the two cell lines.
www.fsigenetics.com/article/S187...
1/6
The DNA of a female murder victim was genotyped and it turns out that she has been a chimera: a mixture of 46XX/46XY cell lines.
The analysis (STR-based) found:
1. The maternal chromosome was identical between the two cell lines.
www.fsigenetics.com/article/S187...
1/6
Forensic analysis of a parthenogenetic 46, XX/46, XY congenital chimera: A case report
In forensic identification, chimerism is an extremely rare phenomenon in which DNA
samples can easily be misidentified as mixtures from two individuals. If only a single
cell population from the chime...
www.fsigenetics.com
January 6, 2026 at 5:38 PM
Crazy interesting biology!
I wonder if there is any phenotypic evidence of this chimerism.
I wonder if there is any phenotypic evidence of this chimerism.
Reposted by Flávia E. Rius
#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/...
github.com/eriksquires/...
GitHub - eriksquires/RStudio_with_Windows
Contribute to eriksquires/RStudio_with_Windows development by creating an account on GitHub.
github.com
December 31, 2025 at 6:51 PM
#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/...
github.com/eriksquires/...
Reposted by Flávia E. Rius
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...
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...
Fast YAML 1.2 Parser and Formatter
A fast, correct, safe, and ergonomic YAML 1.2 parser and generator written in Rust. Convert between YAML and simple R objects with full support for multi-document streams, tags, anchors, and aliases. ...
posit-dev.github.io
December 16, 2025 at 1:54 PM
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...
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...
Reposted by Flávia E. Rius
polars-bio—fast, scalable and out-of-core operations on large genomic interval datasets academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/biodatageeks...
December 3, 2025 at 5:16 PM
polars-bio—fast, scalable and out-of-core operations on large genomic interval datasets academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/biodatageeks...
Reposted by Flávia E. Rius
Tech I'm thankful for blog.stephenturner.us/p/tech-im-th... #rstats 🧬🖥️🧪
Tech I'm thankful for (2024)
Data science and bioinformatics tech I'm thankful for in 2024: tidyverse, RStudio, Positron, Bluesky, blogs, Quarto, bioRxiv, LLMs for code, Ollama, Seqera Containers, StackOverflow, ...
blog.stephenturner.us
November 25, 2024 at 2:29 PM
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
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
November 11, 2025 at 1:44 PM
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
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
Reposted by Flávia E. Rius
🧬 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
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
November 6, 2025 at 2:27 PM
🧬 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
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.
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.
1/ 🚨New paper in Nature Genetics
Genetic factors are associated with the educational fields people study, from arts to engineering.
Article: www.nature.com/articles/s41...
FAQ: www.thehastingscenter.org/genomic-find...
Genetic factors are associated with the educational fields people study, from arts to engineering.
Article: www.nature.com/articles/s41...
FAQ: www.thehastingscenter.org/genomic-find...
Genetic associations with educational fields - Nature Genetics
Genome-wide analyses of 10 educational fields identify 17 associated loci. Analysis of genetic clustering across specializations identifies two key dimensions that show genetic overlap with personalit...
www.nature.com
November 4, 2025 at 2:40 PM
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.
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.
The solution is educating health professionals to communicate PRS risk (and other risks) clearly.
🧬 PRSs in practice (1/5): Public understanding — are we underestimating the public?
A common claim: “The public won’t understand polygenic risk scores (PRSs)” — so using them in healthcare could be risky.
But is that really true? 🧵
A common claim: “The public won’t understand polygenic risk scores (PRSs)” — so using them in healthcare could be risky.
But is that really true? 🧵
November 3, 2025 at 5:49 PM
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.
The solution is educating health professionals to communicate PRS risk (and other risks) clearly.
Reposted by Flávia E. Rius
4 word horror story for an R user:
"has a Java dependency"
"has a Java dependency"
October 12, 2025 at 4:29 PM
4 word horror story for an R user:
"has a Java dependency"
"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.
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.
October 11, 2025 at 12:19 AM
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.
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.
Reposted by Flávia E. Rius
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. 🧵
Let’s talk about the curse of dimensionality in bioinformatics—and why it’s not just a math problem, it’s a biological one. 🧵
October 9, 2025 at 1:15 PM
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. 🧵
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!
September 27, 2025 at 4:28 PM
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!
Reposted by Flávia E. Rius
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’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 👋
Content – Beatriz Milz
beamilz.com
October 29, 2024 at 2:52 AM
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’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
Completely recommend!
github.com/A2-ai/rv
#rstats
GitHub - A2-ai/rv
Contribute to A2-ai/rv development by creating an account on GitHub.
github.com
August 24, 2025 at 3:37 PM
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
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...
Especially beginner to intermediate-level ones.
www.tidyverse.org/blog/2017/12...
Project-oriented workflow
Advice on workflows for developing R scripts. How to think about whether an action belongs in the script or elsewhere.
www.tidyverse.org
August 1, 2025 at 8:37 PM
Every #Rstats user should read this post from @jennybryan.bsky.social.
Especially beginner to intermediate-level ones.
www.tidyverse.org/blog/2017/12...
Especially beginner to intermediate-level ones.
www.tidyverse.org/blog/2017/12...