Lorena Pantano

GitHub - jonasscheid/claude-nfcore-plugin Contribute to jonasscheid/claude-nfcore-plugin development by creating an account on GitHub.

If you use #claudeai and develop #nf-core, this is a good set of skills that will save you time: github.com/jonasscheid/... Thanks Jonas Scheid.

Iceberg diagram illustrating hidden complexities in biobank data: visible raw data above the waterline, and three categories of hidden challenges below: batch effects, population stratification, and inaccurate phenotype data.

🧬💻 Before you touch any code in a biobank analysis, you need to answer two questions: what's your research question, and who's your audience?

My new blog series on the BWIB blog starts there.
🔗 boston-wib.org/blog/biobank...

We solved multi-collaborator genomics data sharing by composing existing tools (IGV), automating format conversion, and deploying via GitHub Actions + AWS (S3 and CloudFront). And minimal authentication with lambda.

youtu.be/_qPsqCyFsgg
substack.com/home/post/p-...

#bioinformatics #genomics

Bringing IGV webapp to Your Cloud Workspace in Seqera Bringing IGV visualization directly to your cloud workspace eliminates the download-to-view cycle

I built an IGV integration for Seqera Studios with automatic track discovery. Spin up a Studio, point it to your Nextflow or nf-core pipeline output, and IGV launches with all compatible files already loaded.

📺 Watch: www.youtube.com/watch?v=eWHC...

After 6 months of work, we're finally launching the Health Integrity Project! 🎉

We built this to fight health misinformation by bridging the gap between scientific research and the public.

Starting w Women's Health Edition 🔬

healthintegrityproject.org

#HealthMisinformation #WomensHealth

A Coffee with CompBio Step into the world where algorithms meet biology! Hosts Lorena Pantano and Alex Bartlett, two dynamic women in science, unravel the complexities and curiosities of computational biology. Each episode...

If you want to hear real life stories about #CompBio, join our Podcast smartlink.ausha.co/a-coffee-wit.... Latest episodes on how to optimize Rmarkdowns for big projects: smartlink.ausha.co/a-coffee-wit... cc Alex Bartlett

Daily reminder to use current tools to save and read data in R.
github.com/qsbase/qs/is...
#r #bioinformatics #compbio #best-practices

@lopantano.bsky.social just presented on unifying community-driven analysis guidelines and templates for data interpretability, showcasing the bcbio-reports project from @hsph.harvard.edu. This infrastructure standardizes multi-omic analysis so researchers can focus on biology. 🧬

A Coffee with CompBio | Ausha Step into the world where algorithms meet biology! Hosts Lorena Pantano and Alex Bartlett, two dynamic women in science, unravel the complexities and curiosities of computational biology. Each episode...

🧬☕ Exciting News!
@abartlett004.bsky.social and I just launched A Coffee with CompBio - a podcast where we dive into the science, stories, and people behind computational biology.

🔗Apple podcasts.apple.com/us/podcast/a...
🔗Spotify open.spotify.com/show/5IF1Z9x...
🌐 podcast.ausha.co/a-coffee-wit...

"You know you're still needed as a bioinformatician when people keep sending you Word documents with code in them. 😅

#Bioinformatics #Code #TechLife"

Using seqera AI to understand nextflow.log, actually it told me where in the nextflow script was the error and I could see the problem was my samplesheet names. I would say this is even a better usage of AI :) @seqera #chipseq @nextflow.io @nf-co.re #troubleshooting to 2min #bioinformatics

Thank you!

If you’re in Boston 🌆 and use #nf-core or #Nextflow, join our regional channel! 🌐 We’re starting monthly meetings 📅 to foster community growth and mutual support! 🤝

nfcore.slack.com/archives/C08...

Thank you, R. Gonzalo Parra 🏳️‍🌈, for making it happen. We should NOT fear to be ourselves. That is why this communication is important. This is the path to a better world where everyone feels welcome. 🙏🏽

When AI Cannibalizes Its Data Podcast Episode · Short Wave · 02/18/2025 · 13m

🎙️Listen to this insightful podcast about current Generative LLM technology. It covers how it behaves with edge cases and when data is insufficient, and clarifies difficult-to-remove biases. These biases affect fields like life-science R&D, the most. #LLM #Biotech
podcasts.apple.com/us/podcast/s...

📊 An interesting study highlights how our reliance on thresholds for gene expression data could lead us to:

• Miss promising new targets 🎯
• Invest resources in suboptimal candidates 💸

#Genomics #Bioinformatics #ResearchInnovation #DataScience
Source: www.biorxiv.org/content/10.1...

Looking forward for the team to bring more people together around this vast effort of making analysis accessible to everyone #bioinformatics

Prepare Reproducible Example Code via the Clipboard Convenience wrapper that uses the rmarkdown package to render small snippets of code to target formats that include both code and output. The goal is to encourage the sharing of small, reproducible, a...

Always learn some new package from #tidyverse. This time reprex to help you with posting when you need help with some code reprex.tidyverse.org/index.html #bestpractices #coding

Just had an epiphany: I'm using GenAI tools to streamline everything—emails, scheduling, even crafting killer playlists. Saved all this time... only to dive into mind games to keep my brain sharp and nimble. Is this peak human irony or what? 🤖🧠 #LifeHacks #BrainTwister 😅

We are having one in Boston, trying to hosting it around cambridge. Stay tune!