HARE v1.2.0

May 8, 2024

New ✨

• Tool support (and test suite) for non-human species, including metazoa, plants, vertebrates, and fungi.
• The example folder is back! Contains a sample script as well as example files so that users know how to format inputs and what outputs to expect.

Fixes 🔧

• Documentation corrections and clarifying instructions for installation and resource downloads.

HARE v1.1.0

January 10, 2024

New ✨

• You can now install dependencies using conda (environment.yml file included) and the hare package using pip for easier and more consistent installation
• As a result, the tool runs smoothly from the command line with commands like hare intersect
• Added unit tests to improve reliability and check installation
• Introduction of the prerank function which allows you to create ranked lists of genes for enrichment analysis in tools like GSEA and WebGestalt
• More options and flags to make runs more flexible and reduce the need to manipulate files upstream of using the pipeline

Fixes 🔧

• Catching various possible failures from dependencies and user inputs and raising errors with clear error messages
• Significance testing is now done with Python packages instead of R, reducing the chance of dependency clashes or run failure

Deprecated 👋

• The directory of example files is gone (you can now test your install with unit testing). If you'd like to see what input and output files look like, you can still review details using the data dictionary (dataDictionary.md)

v1.0.0

Version 1 of the HARE pipeline allows users to input GWAS summary statistics and perform enrichment analysis by looking for intersections with genetic features in a specified BED file. The tool uses a Python script to generate a list of intersections and computes intersections/bp as an output statistic. HARE includes an R script for processing results/hypothesis testing.

This release was used to generate the results seen in the Kun, et al., 2023 publication.