Flávia E. Rius

4 word horror story for an R user:

"has a Java dependency"

- first thing needed (told last here bc you may already know, even if I didn't) is at least a superficial understanding of the concept of tokens and how it may limit your output (you can find the limit empirically, depending on the application).

My takes on doing this for the 1st time on Gemini 2.5 Pro, to extract info from unstructured data, are:

- makes a difference if you submit csv or tsv file (the latter was better);
- depending of the day it will be able to process more or less data (timeout varies due to server load variability);

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 👋

GitHub - A2-ai/rv Contribute to A2-ai/rv development by creating an account on GitHub.

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

True story. So hard to fix this!

Project-oriented workflow Advice on workflows for developing R scripts. How to think about whether an action belongs in the script or elsewhere.

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 forgotten half of scientific thinking | PNAS The forgotten half of scientific thinking

“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

Monash IVF admits second major embryo mix up Reproductive giant Monash IVF has released a statement confirming a second major mishap where a woman received the wrong embryo.

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.

I’m so sorry about that, Dariia. Stay safe!

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

To clarify, it is not present in base R. Only when loading {data.table}.

Sorry for my poor phrasing!

Yes, this is something I already knew! But I got surprised especially because I use {data.table} a lot, and it is already there, you know? Easier than setting up my own %notin% operator.

Thanks for sharing, though!

It is from library(data.table).

Sorry, I got so excited that I did not polish my writing to become clearer 😅.

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