expressrna.org/polyAI

polyAI: a deep learning model that predicts where a transcript is cleaved and polyadenylated, from sequence alone. Trained on 1.6 billion Nanopore direct-RNA reads. Paste a sequence or a human gene.

expressrna.org/polyAI

#polyAI #polyAtlas #expressRNA

🧬 polyAtlas update: a 3′-end atlas from public direct-RNA long-read data.

Six species: human, mouse, yeast, rice, Arabidopsis and C. elegans.

Improved sample annotation, so you can now compare site usage across tissues

expressrna.org/polyAtlas

#expressRNA #polyAtlas #DirectRNA #bioinformatics

expressRNA presents polyAtlas: taking all human #Nanopore direct-RNA sequencing data and building an atlas (map of RNA molecule endings), annotated by cell line.

www.expressrna.org/polyAtlas

Every transcript has an ending. Not every ending is the same.

#expressRNA #polyAtlas #Nanopore #directRNA

🧬 New in expressRNA: all work and no play makes expressRNA ... have fun with PacMan and see how many RNA-binding motifs and polyadenylation signals you can catch! If you are registered, you get an entry on the top score board!

Start here: www.expressrna.org/index.html?a...

#expressRNA #pacman #fun

It would have been great to present #expressRNA and #spatialAPA at @scverse.bsky.social in Copenhagen, but somehow just realised too late. Next year!

expressrna.org

#expressRNA #scverse2026 #spatialAPA

🧬 New in expressRNA: MCP, so you can "talk" with expressRNA, find out analyses, results, discover how bioinformatics is done on the platform and more. Open you expressRNA profile where you can find MCP URL and token to connect it to Claude, ChatGPT or another LLM.

#expressRNA #MCP #AI #LLM

New in expressRNA: native iCLIP analysis. Upload FASTQ — nf-core/clipseq + iCount run as a real Nextflow pipeline: crosslink/peak calling, motif discovery, live genome browser.

expressrna.org

#iCLIP #bioinformatics #clip #expressRNA

🧬 New in expressRNA: scanRBP — predict which RNA-binding proteins bind your sequence. Paste it in, get an interactive clustered heatmap across 1000+ RBP motifs (mCross + CISBP-RNA). Free, no install.

Try it: www.expressrna.org/index.html?a...

#bioinformatics #expressRNA

🧬 New in expressRNA: RNAmotifs2 cluster motif analysis. Auto-runs on every APA analysis, or upload your own splicing/polyA event table. Enriched motif clusters + RNA-maps, FDR & permutation stats.

Live example: www.expressrna.org/index.html?a...

Built on RNAmotifs2: github.com/grexor/rnamo...

Also: alternative splicing analysis via splicekit (github.com/bedapub/spli...) has been live since July.

Try it: expressrna.org — get in touch if you'd like your data analyzed on the platform :-)

#transcriptomics #bioinformatics #spatialAPA #expressRNA

August was good to #expressRNA: two new analysis types.

🗺️ Spatial Patterns — compare polyA usage & expression across multiple Visium sections between conditions (v1 + v2)

📈 Gene expression time courses from RNA-seq — plot expression across your own ordered sample sequence

💡 Importing a full sample set from ArrayExpress (with annotation) into expressRNA just needs a project ID (PRJNA or similar).

#transcriptomics #bioinformatics #expressRNA

New in expressRNA: Gene Expression Time Course 😀

Arrange samples into your own ordered sequence — dev stages, a time series, treatment steps — then plot how one or more genes' expression unfolds across it (CPM/log2CPM). 🧵👇

working on expressRNA 😀

expressrna.org

expressRNA — an open, free platform for post-transcriptional RNA regulation research, at this stage mostly alternative polyadenylation.

Data upload -> quantify polyA sites -> differential analyses -> CLIP-seq RNA-maps

#expressRNA #transcriptomics #RNAseq #alternativepolyadenylation