Fuzzy-Onions - Helper scripts for the FlyBase scRNAseq project

Fuzzy-Onions (fzo) is a set of Python modules and helper scripts to facilitate the annotation and curation of single-cell RNA-seq (scRNAseq) datasets for exploitation by FlyBase.

Setup

Fuzzy-Onions is currently not available on PyPI, and will likely never be due to its highly specific nature.

Clone the repository locally, then run uv sync from within the local copy:

$ git clone https://github.com/FlyBase/fuzzy-onions.git
$ cd fuzzy-onions
$ uv sync

The tool can then be invoked through UV as follows:

$ uv run fzo --help

or, if you are not within the fuzzy-onions directory:

$ uv --project /path/to/fuzzy-onions run fzo --help

I recommend setting up an alias like:

alias fzo="uv --project /path/to/fuzzy-onions run fzo"

so that you can simply call fzo from anywhere:

$ fzo --help

Configuration

Fuzzy-Onions expects a configuration file under the name $XDG_CONFIG_HOME/fuzzyonions/config (on GNU/Linux) or ~/Library/Application Support/fuzzyonions/config (on Mac OS).

Here is a minimal sample configuration file:

[store]
production: <path to a directory containing the datasets>
staging: <same, but for datasets from the staging server>

[curation]
proformae: <path to a directory containing FlyBase's proformae files>

See the example configuration file for more details about the contents of that file.

Basic usage

Call fzo -h to get a list of the available subcommands, and fzo <subcommand> -h to get the help message for a given subcommand.

The main commands are:

• store, to manage the local cache of datasets;

• explorer, to enter a mode allowing to interactively explore the contents of a dataset;

• curate, to produce a proforma or a summarised expression table from a dataset.

• discover, to automatically discover newly published scRNAseq papers.

• tracker, to keep track of the datasets and their status.

Copying

Fuzzy-Onions is distributed under the terms of the MIT license.