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Flávia E. Rius @flaviaerius.bsky.social · 1d

- 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).

Flávia E. Rius @flaviaerius.bsky.social · 1d

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);

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Flávia E. Rius @flaviaerius.bsky.social · 1d

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.

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Reposted by Flávia E. Rius

Ming Tommy Tang @tommytang.bsky.social · 3d

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. 🧵

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Flávia E. Rius @flaviaerius.bsky.social · 14d

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!

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Reposted by Flávia E. Rius

Beatriz Milz @beamilz.com · Oct 29

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 👋

Content – Beatriz Milz

beamilz.com

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Flávia E. Rius @flaviaerius.bsky.social · Aug 24

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

GitHub - A2-ai/rv

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

github.com

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Flávia E. Rius @flaviaerius.bsky.social · Aug 2

True story. So hard to fix this!

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Flávia E. Rius @flaviaerius.bsky.social · Aug 1

Every #Rstats user should read this post from @jennybryan.bsky.social‬.
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

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Reposted by Flávia E. Rius

Dr Emma Hodcroft @firefoxx66.bsky.social · Jul 25

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

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Flávia E. Rius @flaviaerius.bsky.social · Jul 16

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

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Reposted by Flávia E. Rius

Ming Tommy Tang @tommytang.bsky.social · Jul 10

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

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Flávia E. Rius @flaviaerius.bsky.social · Jul 7

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

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Reposted by Flávia E. Rius

Ardem Patapoutian @ardemp.bskyverified.social · Jun 26

“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/...

The forgotten half of scientific thinking | PNAS

The forgotten half of scientific thinking

www.pnas.org

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Flávia E. Rius @flaviaerius.bsky.social · Jun 11

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

1

Reposted by Flávia E. Rius

Shai Carmi @shaicarmi.bsky.social · Jun 10

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...

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.

thenightly.com.au

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Flávia E. Rius @flaviaerius.bsky.social · Jun 6

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.

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Flávia E. Rius @flaviaerius.bsky.social · Jun 5

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

Flávia E. Rius @flaviaerius.bsky.social · Jun 5

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

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Flávia E. Rius @flaviaerius.bsky.social · Jun 5

jq is so useful.

Flávia E. Rius @flaviaerius.bsky.social · May 27

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

Flávia E. Rius @flaviaerius.bsky.social · May 23

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.

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Flávia E. Rius @flaviaerius.bsky.social · May 22

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.

Reposted by Flávia E. Rius

Dariia Mykhailyshyna @dariia.bsky.social · May 21

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

Dariia Mykhailyshyna @dariia.bsky.social · May 9

❗️Our next workshop will be on May 22nd, 6 pm CEST, on Power Bpy: python package for automating and accelerating Power BI dashboard development by
@rshean.bsky.social!
Register or sponsor a student by donating to support Ukraine!
Details: bit.ly/3wBeY4S
Please share!
#AcademicSky #EconSky #Python

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Flávia E. Rius @flaviaerius.bsky.social · May 22

To clarify my poor post, it is NOT present in base R. Only when loading {data.table}.

Still exciting for me, though!

#rstats

Flávia E. Rius @flaviaerius.bsky.social · May 21

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

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