We are excited to share our online book and preprint on “Orchestrating Spatial Transcriptomics Analysis with Bioconductor”!
Interested in learning about the single cell advances? Tune in to this event from SatijaLab. satijalab.org/scgd #SingleCell 🧬🖥️
Lukas Weber
Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools. #GeneExpression #SingleCell #scRNAseq #NAR 🧬 🖥️
academic.oup.com/nar/advance-...
Noor (@noorpratap.bsky.social) has been working on this for quite some time! It took a bit of work to figure out, but now you can map your scATAC-seq reads directly to the genome and sort and dedup them with alevin-fry-atac. You get a BED file with counts ready for downstream analysis! 1/
Thank you @training.ebi.embl.org for putting together an insightful program and bringing in a very diverse group of participants, both in terms of countries and experience levels. I'm leaving with a rich support network who were all readily sharing ideas and solutions.
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8
Biologist, stop putting UMAP plots in papers!
Blogpost here: simplystatistics.org/posts/2024-1...
🎆4 years in the making! Thrilled to share the 1st spatial single cell aging clock ⏰ www.nature.com/articles/s41...
We use #AI + spatial transcriptomics to discover what makes some cells age faster/slower in the brain 🧠
Led by Eric Sun and awesome collaboration w/ @brunetlab.bsky.social🧵
Rob Patro
Rafael Irizarry
After 4y in the making, I am super excited that my main PhD project is published 🎉🥳🎉🎉🥳
www.nature.com/articles/s41...
LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space.
Some highlights⬇️
UMAP is a powerful tool for exploratory data analysis, but without a clear understanding of how it works, it can easily lead to confusion and misinterpretation.
Abstract. Bgee (https://www.bgee.org/) is a database to retrieve and compare gene expression patterns in multiple animal species. Expression data are integ
Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment https://www.biorxiv.org/content/10.1101/2024.11.27.625771v1
Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
bioRxiv Bioinfo
Thank you to all the trainers and participants who have joined us for our last event of the year, 'Managing a bioinformatics core facility'.
If you're interested in learning from like-minded peers, sign up for alerts for the next edition: mailchi.mp/ebi/cor_alerts
#Bioinformatics #CoreFacility
🧬🥼
The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...
I was loving Claude Code... until I tried it with #rstats. Constant errors, wouldn't use the tidyverse even when asked, "optimized" functions were slower.
Frustrated, I started a session just to teach R to Claude and summarize what it learned into a CLAUDE.md file gist.github.com/sj-io/3828d6...
EMBL-EBI Training
sarah
Ultrafast mapping of short reads to transcriptomic and metagenomic references via lightweight mappin
