# bakana-remotes

> Fetch remote single-cell RNA-seq datasets for input into the bakana analysis pipeline.

Latest version **2.2.2** (published 2026-09-20) · MIT license · 0 weekly downloads

## Install

```sh
npm install bakana-remotes
pnpm add bakana-remotes
yarn add bakana-remotes
bun add bakana-remotes
```

## Health

**Score 65/100 (B)** — status: active.

Positive: esm support; no vulnerabilities; has provenance; recently updated; high maintenance score.

Warnings: low downloads; no types.

## Facts

| | |
|---|---|
| Version | 2.2.2 |
| Published | 2026-09-20 |
| First published | 2022-10-24 |
| Weekly downloads | 0 |
| License | MIT |
| TypeScript types | none |
| Module format | ESM + CommonJS |
| Dependencies | 3 |
| Unpacked size | 17.3 KB |
| Known vulnerabilities | 0 |
| Install scripts | no |
| Provenance | attested (GitHub Actions) |
| GitHub stars | 0 |
| Author | Aaron Lun |
| Maintainers | ltla |
| Keywords | bioinformatics, single-cell, scRNA-seq |

## Links

- npm: https://www.npmjs.com/package/bakana-remotes
- Repository: https://github.com/kanaverse/bakana-remotes
- Homepage: https://github.com/kanaverse/bakana-remotes#readme
- Issues: https://github.com/kanaverse/bakana-remotes/issues
- npm.io page: https://npm.io/package/bakana-remotes

## Dependencies (3)

- [bakana](https://npm.io/package/bakana.md) ^3.1.0
- [scran.js](https://npm.io/package/scran.js.md) ^4.0.0
- [bioconductor](https://npm.io/package/bioconductor.md) ^0.4.0

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## Recent versions

- 2.2.2 (latest) — 2026-09-20
- 2.2.1 — 2025-08-06
- 2.2.0 — 2025-08-05
- 2.1.0 — 2024-05-05
- 2.0.0 — 2023-07-25
- 2.0.0-alpha.1 — 2023-07-22
- 1.0.3 — 2023-05-01
- 1.0.2 — 2023-04-06
- 1.0.1 — 2023-04-05
- 1.0.0 — 2023-03-10
- 1.0.0-alpha.4 — 2023-03-03
- 1.0.0-alpha.3 — 2023-03-01
- 1.0.0-alpha.2 — 2023-02-26
- 1.0.0-alpha.1 — 2023-01-27
- 0.2.0 — 2022-11-02
- … 2 more at https://npm.io/package/bakana-remotes/versions

## README

# Remote readers for bakana

![Unit tests](https://github.com/kanaverse/bakana-remotes/actions/workflows/run-tests.yaml/badge.svg)
![Documentation](https://github.com/kanaverse/bakana-remotes/actions/workflows/build-docs.yaml/badge.svg)
![NPM](https://img.shields.io/npm/v/bakana-remotes)

## Overview

This package provides a variety of remote readers for the [**bakana**](https://npmjs.org/package/bakana) package,
allowing us to perform scRNA-seq analyses on datasets from other sources.
Currently we support:

- [**takane**](https://github.com/ArtifactDB/takane)-formatted -`SummarizedExperiment` objects in the [**gypsum**](https://github.com/ArtifactDB/gypsum-worker) bucket.
- [**takane**](https://github.com/ArtifactDB/takane)-formatted -`SummarizedExperiment` objects via the [**SewerRat**](https://github.com/ArtifactDB/gypsum-worker) API.

## Quick start

Usage is as simple as:

```js
import * as remotes from "bakana-remotes";
import * as bakana from "bakana";

// Add desired readers for unserialization.
bakana.availableReaders["gypsum"] = remotes.GypsumDataset;
```

For **gypsum**-sourced datasets, we can construct the following object, which uses the Zeisel brain single-cell dataset from 2015:

```js
let gyp = new remotes.GypsumDataset("scRNAseq", "zeisel-brain-2015", "2023-12-14");
```

Similarly, **SewerRat**-sourced datasets can be pulled from shared filesystems (e.g., on HPCs) using the following:

```js
let sewer = new remotes.SewerRatDataset(
    "/path/to/dataset", 
    url = "https://somewhere.edu/sewerrat"
);
```

These objects can then be used in an entry of `datasets` in [`bakana.runAnalysis()`](https://ltla.github.io/bakana/global.html#runAnalysis).

We also provide the equivalent `Result` objects, if users just want to read existing analysis results:

```js
let gyp2 = new remotes.GypsumResult(
    "scRNAseq", 
    "ernst-spermatogenesis-2019", 
    "2023-12-21",
    path = "emptydrop"
);

let sewer2 = new remotes.SewerRatResult(
    "/path/to/result", 
    url = "https://somewhere.edu/sewerrat"
);
```

Check out the [API documentation](https://kanaverse.github.io/bakana-remotes) for more details. 

## Links

See the [**bakana**](https://github.com/kanaverse/bakana) documentation for more details on how to create a 
[custom `Dataset` reader](https://github.com/kanaverse/bakana/blob/master/docs/related/custom_readers.md).
Implementations of readers for other databases are welcome.

---
_Source: https://npm.io/package/bakana-remotes · Machine-readable twin of the npm.io package page. Health data is recomputed on every publish._