gwas2crispr

0.1.5

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

0packages depend

5.2Kdownloads / year

85.9%test coverage

13/13checks pass

Overview

About

Maintained by Othman S. I. MohammedFirst published 2025-08-223 releasesCRAN page ↗GitHub ↗

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 using supported trait identifiers, 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. The existing efo_id argument is retained for backward compatibility. The package prepares computational artifacts for downstream workflows; it does not perform biological causality testing, clinical interpretation, therapeutic design, or wet-lab validation. 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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)openSUSE (OBS)

install.packages("gwas2crispr", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("leopard0ly/gwas2crispr")

Development version from leopard0ly/gwas2crispr. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-gwas2crispr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-gwas2crispr

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 1.3 min · r-oldrel-macos-x86_64

Check history

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

Documentation signals are not tracked yet for this package.

Downloads

5.2K

CRAN downloads in the past year

Rank #7,885 · ~14/day · ~433/mo

gwas2crispr Releases R versions

Daily download trend is not available in this view yet.

26230 days

1.3K90 days

5.2K1 year

Compare downloads with other packages →

Also on77 r2u18 autocran

Repository

GitHub ↗ leopard0ly/gwas2crispr

0Stars

0Forks

0Open issues

0Open PRs

3Releases

48Commits

2Contributors

48 commits · Last activity 2026-06-02

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/leopard0ly/gwas2crispr on 2026-07-19.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1

Imports (8)

httr dplyr purrr tibble tidyr readr stringr tidyselect

LinkingTo (0)

none

Suggests (7)

Biostrings BSgenome.Hsapiens.UCSC.hg38 GenomeInfoDb optparse testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Othman S. I. Mohammed

Author, Maintainer

Authors (1)

Othman S. I. Mohammed

Author, Maintainer

LEOPARD.LY LTD

Package Timeline

3 releases. R releases are shown for context.

0.1.5Latest
2026-06-02 · current release · diff ↗
0.1.4
2026-05-10 · diff ↗
R
R 4.6.0 released · 2026-04-24
0.1.2
2026-03-10
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-08-22
Total releases: 3 / 1 yrs
License: MIT + file LICENSE OSI
Download size: 21 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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