Remote readers for bakana

!Unit tests
!Documentation
!NPM

Overview

This package provides a variety of remote readers for the bakana package,
allowing us to perform scRNA-seq analyses on datasets from other sources.
Currently we support:

- takane-formatted -SummarizedExperiment objects in the gypsum bucket.
- takane-formatted -SummarizedExperiment objects via the SewerRat 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().

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 for more details.

Links

See the bakana documentation for more details on how to create a
custom Dataset` reader.
Implementations of readers for other databases are welcome.