From 943ed9ef6656af5eae1bfc7ed233d77615cae210 Mon Sep 17 00:00:00 2001 From: Benjamin Chu Date: Mon, 4 Mar 2024 12:22:00 -0800 Subject: [PATCH] update software/paper links in docs --- docs/src/man/download.ipynb | 4 ++-- docs/src/man/download.md | 4 ++-- docs/src/man/intro.ipynb | 6 +++--- docs/src/man/intro.md | 6 +++--- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/docs/src/man/download.ipynb b/docs/src/man/download.ipynb index c649a974..9de0068c 100644 --- a/docs/src/man/download.ipynb +++ b/docs/src/man/download.ipynb @@ -10,9 +10,9 @@ "\n", "## Software\n", "\n", - "| Operating System | v0.1.0 (Pre-release, 19 Feb, 2024) |\n", + "| Operating System | v0.1.1 (March 4th, 2024) |\n", "| :--- | :----: |\n", - "| Linux 64-bit | [Download](https://github.com/biona001/GhostKnockoffGWAS/releases/tag/v0.1.0) |\n", + "| Linux 64-bit | [Download](https://github.com/biona001/GhostKnockoffGWAS/releases/tag/v0.1.1) |\n", "\n", "After unzipping, the executable will be located inside `bin/GhostKnockoffGWAS`. We recommend adding the folder containing the `GhostKnockoffGWAS` executable to `PATH` for easier access." ] diff --git a/docs/src/man/download.md b/docs/src/man/download.md index 3f300d48..5685d589 100644 --- a/docs/src/man/download.md +++ b/docs/src/man/download.md @@ -5,9 +5,9 @@ Here is the main downloads page. New software and pre-processed knockoff data wi ## Software -| Operating System | v0.1.0 (Pre-release, 19 Feb, 2024) | +| Operating System | v0.1.1 (March 4th, 2024) | | :--- | :----: | -| Linux 64-bit | [Download](https://github.com/biona001/GhostKnockoffGWAS/releases/tag/v0.1.0) | +| Linux 64-bit | [Download](https://github.com/biona001/GhostKnockoffGWAS/releases/tag/v0.1.1) | After unzipping, the executable will be located inside `bin/GhostKnockoffGWAS`. We recommend adding the folder containing the `GhostKnockoffGWAS` executable to `PATH` for easier access. diff --git a/docs/src/man/intro.ipynb b/docs/src/man/intro.ipynb index a152dd21..eb902ada 100644 --- a/docs/src/man/intro.ipynb +++ b/docs/src/man/intro.ipynb @@ -8,11 +8,11 @@ "\n", "This package conducts knockoff-based inference to perform genome-wide conditional independent tests based on GWAS summary statistics. The methodology is described in the following papers\n", "\n", - "> Chen Z, He Z, Chu BB, Gu J, Morrison T, Sabatti C, Candes C. \"Controlled Variable Selection from Summary Statistics Only? A Solution via GhostKnockoffs and Penalized Regression\", arXiv preprint arXiv:2402.12724 (2024).\n", + "> Chen Z, He Z, Chu BB, Gu J, Morrison T, Sabatti C, Candes C. \"Controlled Variable Selection from Summary Statistics Only? A Solution via GhostKnockoffs and Penalized Regression\", arXiv preprint arXiv:2402.12724 (2024); doi: [https://doi.org/10.48550/arXiv.2402.12724](https://doi.org/10.48550/arXiv.2402.12724)\n", "\n", - "> Chu BB, Gu J, Chen Z, Morrison T, Candes E, He Z, Sabatti C. (2023). Second-order group knockoffs with applications to GWAS. arXiv preprint arXiv:2310.15069.\n", + "> Chu BB, Gu J, Chen Z, Morrison T, Candes E, He Z, Sabatti C. (2023). Second-order group knockoffs with applications to GWAS. arXiv preprint arXiv:2310.15069; doi: [https://doi.org/10.48550/arXiv.2310.15069](https://doi.org/10.48550/arXiv.2310.15069)\n", "\n", - "> 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. \n", + "> 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](https://doi.org/10.1101/2024.02.28.582621)\n", "\n", "The main working assumption is that we do not have access to individual level genotype or phenotype data. Rather, for each SNP, we have its Z-scores with respect to some phenotype from a GWAS, and access to LD (linkage disequilibrium) data. The user is expected supply the Z-scores, while we supply the LD data in addition to some pre-computed knockoff data." ] diff --git a/docs/src/man/intro.md b/docs/src/man/intro.md index f3f4c69c..22b7a3b3 100644 --- a/docs/src/man/intro.md +++ b/docs/src/man/intro.md @@ -3,11 +3,11 @@ This package conducts knockoff-based inference to perform genome-wide conditional independent tests based on GWAS summary statistics. The methodology is described in the following papers -> Chen Z, He Z, Chu BB, Gu J, Morrison T, Sabatti C, Candes C. "Controlled Variable Selection from Summary Statistics Only? A Solution via GhostKnockoffs and Penalized Regression", arXiv preprint arXiv:2402.12724 (2024). +> Chen Z, He Z, Chu BB, Gu J, Morrison T, Sabatti C, Candes C. "Controlled Variable Selection from Summary Statistics Only? A Solution via GhostKnockoffs and Penalized Regression", arXiv preprint arXiv:2402.12724 (2024); doi: [https://doi.org/10.48550/arXiv.2402.12724](https://doi.org/10.48550/arXiv.2402.12724) -> Chu BB, Gu J, Chen Z, Morrison T, Candes E, He Z, Sabatti C. (2023). Second-order group knockoffs with applications to GWAS. arXiv preprint arXiv:2310.15069. +> Chu BB, Gu J, Chen Z, Morrison T, Candes E, He Z, Sabatti C. (2023). Second-order group knockoffs with applications to GWAS. arXiv preprint arXiv:2310.15069; doi: [https://doi.org/10.48550/arXiv.2310.15069](https://doi.org/10.48550/arXiv.2310.15069) -> 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](https://doi.org/10.1101/2024.02.28.582621) The main working assumption is that we do not have access to individual level genotype or phenotype data. Rather, for each SNP, we have its Z-scores with respect to some phenotype from a GWAS, and access to LD (linkage disequilibrium) data. The user is expected supply the Z-scores, while we supply the LD data in addition to some pre-computed knockoff data.