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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.

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.