gwas2crispr: GWAS-to-CRISPR Data Pipeline for High-Throughput SNP TargetExtraction
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 + fileLICENSE |
| URL: | https://github.com/leopard0ly/gwas2crispr |
| NeedsCompilation: | no |
| Language: | en-US |
| Citation: | gwas2crispr citation info |
| Materials: | README,NEWS |
| CRAN checks: | gwas2crispr results |
Documentation:
Downloads:
Linking:
Please use the canonical formhttps://CRAN.R-project.org/package=gwas2crisprto link to this page.