gwas2crispr: GWAS-to-CRISPR Data Pipeline for High-Throughput SNP Target Extraction

Provides a reproducible pipeline to conduct genome‑wide association studies (GWAS) and extract single‑nucleotide polymorphisms (SNPs) for a human trait or disease. Given aggregated GWAS dataset(s) and a user‑defined significance threshold, the package retrieves significant SNPs from the GWAS Catalog and the Experimental Factor Ontology (EFO), annotates their gene context, and can write a harmonised metadata table in comma-separated values (CSV) format, genomic intervals in the Browser Extensible Data (BED) format, and sequences in the FASTA (text-based sequence) format with user-defined flanking regions for clustered regularly interspaced short palindromic repeats (CRISPR) guide design. For details on the resources and methods see: Buniello et al. (2019) <doi:10.1093/nar/gky1120>; Sollis et al. (2023) <doi:10.1093/nar/gkac1010>; Jinek et al. (2012) <doi:10.1126/science.1225829>; Malone et al. (2010) <doi:10.1093/bioinformatics/btq099>; Experimental Factor Ontology (EFO) <https://www.ebi.ac.uk/efo>.

Version:	0.1.2
Depends:	R (≥ 4.1)
Imports:	httr, dplyr, purrr, tibble, tidyr, readr, methods
Suggests:	gwasrapidd, Biostrings, BSgenome.Hsapiens.UCSC.hg38, optparse, testthat, knitr, rmarkdown
Published:	2025-08-22
DOI:	10.32614/CRAN.package.gwas2crispr
Author:	Othman S. I. Mohammed [aut, cre], LEOPARD.LY LTD [cph]
Maintainer:	Othman S. I. Mohammed <admin at leopard.ly>
BugReports:	https://github.com/leopard0ly/gwas2crispr/issues
License:	MIT + file LICENSE
URL:	https://github.com/leopard0ly/gwas2crispr
NeedsCompilation:	no
Language:	en-US
Citation:	gwas2crispr citation info
Materials:	README, NEWS
CRAN checks:	gwas2crispr results

Documentation:

Reference manual:	gwas2crispr.html , gwas2crispr.pdf
Vignettes:	gwas2crispr: From GWAS to CRISPR-ready files (hg38) (source, R code)

Downloads:

Package source:	gwas2crispr_0.1.2.tar.gz
Windows binaries:	r-devel: gwas2crispr_0.1.2.zip, r-release: not available, r-oldrel: gwas2crispr_0.1.2.zip
macOS binaries:	r-release (arm64): gwas2crispr_0.1.2.tgz, r-oldrel (arm64): not available, r-release (x86_64): gwas2crispr_0.1.2.tgz, r-oldrel (x86_64): gwas2crispr_0.1.2.tgz

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