Package: gwas2crispr
Type: Package
Title: GWAS-to-CRISPR Data Pipeline for High-Throughput SNP Target
        Extraction
Version: 0.1.2
Authors@R: c(person(given = "Othman S. I.", family = "Mohammed", email = "admin@leopard.ly", role = c("aut", "cre")), person(given = "LEOPARD.LY LTD", role = "cph"))
Description: 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>.
License: MIT + file LICENSE
URL: https://github.com/leopard0ly/gwas2crispr
BugReports: https://github.com/leopard0ly/gwas2crispr/issues
Depends: R (>= 4.1)
Imports: httr, dplyr, purrr, tibble, tidyr, readr, methods
Suggests: gwasrapidd, Biostrings, BSgenome.Hsapiens.UCSC.hg38,
        optparse, testthat, knitr, rmarkdown
VignetteBuilder: knitr, rmarkdown
Encoding: UTF-8
Language: en-US
RoxygenNote: 7.3.2
biocViews: Software, Genetics, VariantAnnotation, SNP, DataImport
NeedsCompilation: no
Packaged: 2025-08-19 14:14:00 UTC; hp
Author: Othman S. I. Mohammed [aut, cre],
  LEOPARD.LY LTD [cph]
Maintainer: Othman S. I. Mohammed <admin@leopard.ly>
Repository: CRAN
Date/Publication: 2025-08-22 18:50:06 UTC
Built: R 4.6.0; ; 2026-04-26 18:51:49 UTC; unix
