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| [![](https://img.shields.io/badge/docs-latest-blue.svg)](https://biona001.github.io/GhostKnockoffGWAS/dev/)| [![build Actions Status](https://github.com/biona001/GhostKnockoffGWAS/actions/workflows/CI.yml/badge.svg)](https://github.com/biona001/GhostKnockoffGWAS/actions) [![CI (Julia nightly)](https://github.com/biona001/GhostKnockoffGWAS/actions/workflows/JuliaNightly.yml/badge.svg)](https://github.com/biona001/GhostKnockoffGWAS.jl/actions/workflows/JuliaNightly.yml) | [![codecov](https://codecov.io/gh/biona001/GhostKnockoffGWAS/branch/main/graph/badge.svg)](https://codecov.io/gh/biona001/GhostKnockoffGWAS) |

This is a package for analyzing summary statistics data from [*genome-wide association studies (GWAS)*](https://en.wikipedia.org/wiki/Genome-wide_association_study) under the statistical *knockoff framework*. Compared to marginal association testing which controls the FWER, the knockoff framework conducts conditional independence testing while controlling the FDR. As a consequence, `GhostKnockoffGWAS` can be both more precise and powerful than current state-of-the-art GWAS+fine-mapping methods. Its detailed evaluations can be found in our [companion paper]().
This is a package for analyzing summary statistics data from [*genome-wide association studies (GWAS)*](https://en.wikipedia.org/wiki/Genome-wide_association_study) under the statistical *knockoff framework*. Compared to marginal association testing which controls the FWER, the knockoff framework conducts conditional independence testing while controlling the FDR. As a consequence, `GhostKnockoffGWAS` can be both more precise and powerful than current state-of-the-art GWAS+fine-mapping methods. Its detailed evaluations can be found in our [companion paper](https://www.biorxiv.org/content/10.1101/2024.02.28.582621v1).

## New users

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If you use `GhostKnockoffGWAS` in your research, please cite the following references:

> He Z, Chu BB, Yang J, Gu J, Chen Z, Liu L, Morrison T, Bellow M, Qi X, Hejazi N, Mathur M, Le Guen Y, Tang H, Hastie T, Ionita-laza, I, Sabatti C, Candes C. "In silico identification of putative causal genetic variants", bioRxiv 2024.
> He Z, Chu BB, Yang J, Gu J, Chen Z, Liu L, Morrison T, Bellow M, Qi X, Hejazi N, Mathur M, Le Guen Y, Tang H, Hastie T, Ionita-laza, I, Sabatti C, Candes C. "In silico identification of putative causal genetic variants", bioRxiv, 2024.02.28.582621; doi: https://doi.org/10.1101/2024.02.28.582621.

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