bakana-remotes
v2.1.0
Published
Fetch remote single-cell RNA-seq datasets for input into the bakana analysis pipeline.
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Remote readers for bakana
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. - Selected count matrices and row/column
DataFrame
s from ExperimentHub. (This is soft-deprecated as the datasets are a subset of those provided via gypsum.)
Quick start
Usage is as simple as:
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:
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:
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:
let gyp2 = new remotes.GypsumDataset(
"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.