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:
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