SigRepo_Server is the server half of SigRepo, a platform for storing, sharing, and comparing omic signatures. It is a reproducible framework for deploying a SigRepo instance — locally or on a Linux-based cloud host — and for interacting with it through a REST API, an R Shiny web interface, and an MCP server for AI agents.
The client half is the SigRepo R package; signatures themselves are represented as R6 objects defined by OmicSignature, our in-house package.
The server is a set of containerized services:
- MySQL database — initializes and manages the SigRepo schema, storing signatures, collections, users, controlled vocabularies (organisms, platforms, sample types, assay types), and gene set resources. Per-signature differential-expression (difexp) tables are held in a companion object store.
- Plumber REST API — the single access path to the data. It defines
the schema, loads reference tables, stores and retrieves difexp
objects, authenticates every call by
api_key, and exposes the analysis endpoints (signature comparison, enrichment) so that analysis runs server-side rather than requiring users to download whole signatures. - Web interface — an
R Shiny
application (
legacy_app/), the interface our instance serves. From the browser you sign in, browse and deposit signatures and collections, browse the controlled vocabularies and gene set resources, and compare signatures. It bind-mounts its source, so a UI change ships with agit pulland a container restart rather than an image build. - MCP server — a Model Context Protocol endpoint that lets AI agents search signatures, retrieve signature context, compare signatures and browse gene sets, grounded in the stored data. It sits behind a rate-limiting reverse proxy and is reachable at https://sigrepo.org/mcp/.
Because analyses are exposed as discrete API endpoints over a common signature representation, additional analysis engines and external gene-set resources can be added as new endpoints without changing the database schema.
Our team runs a SigRepo server on DigitalOcean.
- To access the signatures and collections stored in our database, VISIT OUR WEBSITE to create an account or CONTACT US to be added.
- To connect and interact with our database using the “SigRepo” R package
- To install a “SigRepo” database instance on your local machine
Beyond storage and retrieval, the API supports analysis over stored signatures:
- Signature comparison — any set of signatures can be compared by feature overlap (Jaccard index with Fisher exact tests), by rank-based Kolmogorov–Smirnov statistics, or by GSEA, returning similarity matrices and, for GSEA, per-pair leading-edge data. Bi-directional signatures are compared per matched group label.
- Gene set enrichment — over-representation and rank-based enrichment against MSigDB via hypeR, with MSigDB collections cached server-side.
Active work, not yet part of the deployed stack:
- Signature enrichment in the web interface — the Shiny Annotate
tab is being rebuilt directly on
hypeR,
so that the tab and the
SigRepoR package run enrichment the same way. The tab shows an under-development page until that rebuild lands; the API’s enrichment endpoints are unaffected. - AI-assisted signature authoring — an agent service that reads a study’s differential-expression output and description, proposes metadata from SigRepo’s controlled vocabularies, and emits a validated OmicSignature for the depositor to review, so contributing a signature becomes a review step rather than a curation task.
- Additional external gene-set resources for matching stored signatures against published gene sets.
See the installation guide for standing up your own
instance. install_sigrepo.sh starts the database and the API, builds
the schema and reference tables, and brings up the Shiny interface. The
stack is defined with docker compose; the MySQL service, the API, the
Shiny interface, and the MCP server each run as their own container on a
shared internal network, with only the intended ports published.