From 9da8854ae4b8f4a65cb131f5eef1081ed4507b3b Mon Sep 17 00:00:00 2001 From: Aadam Date: Fri, 30 Aug 2024 10:58:51 -0400 Subject: [PATCH] Update README.md --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index 7a9870f..a739df0 100644 --- a/README.md +++ b/README.md @@ -5,3 +5,7 @@ [![Build Status](https://github.com/aadimator/ISCHIA.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/aadimator/ISCHIA.jl/actions/workflows/CI.yml?query=branch%3Amain) [![Coverage](https://codecov.io/gh/aadimator/ISCHIA.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/aadimator/ISCHIA.jl) [![Aqua](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl) + +This package is a reimplementation of the ISCHIA LR interaction algorithm in Julia. The original implementation is in R and can be found [here](https://github.com/ati-lz/ISCHIA). The algorithm is described in the paper [Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA)](https://www.embopress.org/doi/full/10.1038/s44320-023-00006-5). + +In the original implementation, the LR interaction part of the algorithm is very slow and can take days to run on large datasets. This package aims to speed up the LR interaction part of the algorithm by using Julia's speed and parallelism. For comparison, the original implementation took almost 3 hours to run on their toy/smaller dataset, while the same dataset took around 6 seconds to run on this package.