Changelog

v2.4.0 — September 26, 2026

MCP for AI agents, faster spatial processing, friendlier tables

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.

v2.3.0 — September 20, 2026

Genome Browser, RNAmotifs2 cluster motif analysis

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.

August 2026

Expression Time Course & multi-section Spatial Patterns

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.

July 2026

Alternative splicing analysis & spatial APA

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.

June 2026

Platform revival & full recode

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.

polyAtlas: polyA site atlases from Nanopore direct RNA sequencing

Name: polyAtlas: human polyA site atlas (Nanopore direct RNA)
Creator: expressRNA
License: https://creativecommons.org/licenses/by/4.0/

polyAtlas is a free collection of polyA (cleavage) site atlases, one per species. The human atlas holds 429,193 sites built from 429 public Oxford Nanopore direct-RNA sequencing runs (58 studies, 1.6 billion reads) on GRCh38. In direct RNA sequencing every read's 3' end is the cleavage site, so no 3'-end library is needed. Browse the sites of any gene, see which runs and cell lines support each site and how usage shifts between them, compare with PolyASite 2.0 and 3.0, inspect the polyA signal in the sequence, open the sites in a genome browser and download the whole atlas. No login is needed.

polyAtlas is part of expressRNA, an open platform for post-transcriptional RNA regulation. Built with polyAbuild.