• MCP for AI agents — expressRNA now exposes a read-only MCP server, so an AI assistant like Claude can look up your samples, libraries, analyses and results directly, and explain exactly how a result was computed instead of just reading back numbers. Result tables can be filtered by significance and gene name, so a large analysis doesn't get cut off arbitrarily. Get your access token from your profile page.
• Spatial Patterns refinements — domain maps are now grouped by condition with a shared color scale and new fill display modes, per-domain effect sizes are shown directly in the results table, detection thresholds are editable, and a data-import bug with headered position files is fixed.
• Import spatial samples from GEO/ENA — paste an accession and expressRNA fetches the FASTQ and position files directly, matching the existing bulk-sample import workflow.
• Friendlier data tables — sample, library, CLIP and analyses tables are now resizable and reorderable with show/hide columns; gene tables on the APA, DGE and iCLIP pages are paginated with instant search instead of one long scroll; every table and edit page now shows its record ID.
• Faster, more reliable background processing — polyA site counting is roughly 10x faster, the analysis worker automatically restarts if it crashes, and a mapping/counting bug affecting some spatial and MDS results is fixed.
• Homepage refresh — the Capabilities section is now icon tiles split into core and newer features, including the new MCP integration.

Every mapped sample now has a Genome Browser tab (built on igv.js) so you can inspect the actual aligned reads, search by gene or jump to a locus, and share the current view as a link — multi-gigabyte CRAM files open instantly via HTTP range requests, no download needed.

RNAmotifs2 cluster motif analysis is now integrated: it searches for clusters of short RNA motifs enriched around regulated splice junctions or polyA sites, with Fisher's exact test and FDR correction. It auto-runs on every finished APA analysis, and a new standalone analysis type lets you upload your own event table.

Expression Time Course plots one or more genes across a library's samples in your own order — developmental stages, a time series, treatment steps — with a "draw a profile" search (find genes matching a hand-drawn pattern) and live GO enrichment.

Spatial Patterns extends Spatial APA to compare multiple Visium sections at once: sections are jointly clustered into shared spatial domains, then tested for differential patterns between two groups in both gene expression and polyA site usage.

Bulk RNA-seq analyses now automatically trigger an alternative splicing pipeline (powered by splicekit) once differential expression is complete, with junction/exon/gene-level results browsable in the analysis view.

Spatial APA is now supported for Visium-style datasets — polyA site usage quantified per barcode directly from BAM files, producing spatially resolved maps comparable across tissue sections.

expressRNA returns with a complete ground-up rewrite: a lightweight Python/SQLite backend and a modern single-page jQuery interface. Highlights: redesigned UI, Google OAuth login with groups and visibility controls, a new Samples upload flow, a revamped Libraries module with polyAsite reference integration, Alternative Polyadenylation analyses with RNA-Map plots and CLIP integration, and a background worker for automated processing.