R, Python, and JavaScript · one verdict

biobouncer

A gate for biological inputs. It checks IDs at the door.

One small API answers "is this a valid identifier?" for gene symbols, ontology terms, variant formats, and database accessions across 50 sources. R, Python, and JavaScript return the same verdict for the same input, enforced by a shared conformance corpus.

R docs → Python docs → JavaScript docs → Demo notebooks →

Three doors

One bouncer, three doors

Same ID, same answer. Pick the language you work in.

The R package

Function reference, a getting-started vignette, and recipes, built with pkgdown.

install.packages("biobouncer")

Enter the R door →

The Python package

Guide, examples, a sources cookbook, and API reference, built with MkDocs.

pip install biobouncer

Enter the Python door →

The JavaScript package

API reference from the TypeScript types, with the README as the guide. Runs in Node and the browser.

npm install biobouncer

Enter the JavaScript door →

Checking modes

Four ways to check

One argument, how, decides how strict and how online the check is.

patternIs it well-formed? Offline, deterministic.

cacheDoes it exist in a pinned snapshot? Offline, reproducible.

remoteDoes it exist right now in the source? Live.

existenceSnapshot if one answers, else remote, else pattern.

How it works

A column in, a verdict out

A messy column goes in; one labeled verdict comes out, identical in R, Python, and JavaScript.

biobouncer takes a messy column of biological identifiers, checks each through one gate with the checking modes, and returns one labeled verdict that is the same in R, Python, and JavaScript. — Validate, normalize, and repair a whole column, not just one field.