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 |
| Reference manual: | gwas2crispr.html , gwas2crispr.pdf |
| Vignettes: |
gwas2crispr: From GWAS to CRISPR-ready files (hg38) (source, R code) |
| Package source: | gwas2crispr_0.1.2.tar.gz |
| Windows binaries: | r-devel: gwas2crispr_0.1.2.zip, r-release: gwas2crispr_0.1.2.zip, r-oldrel: gwas2crispr_0.1.2.zip |
| macOS binaries: | r-release (arm64): gwas2crispr_0.1.2.tgz, r-oldrel (arm64): gwas2crispr_0.1.2.tgz, r-release (x86_64): gwas2crispr_0.1.2.tgz, r-oldrel (x86_64): gwas2crispr_0.1.2.tgz |
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