NEWS.md

In gwas2crispr: GWAS-to-CRISPR Data Pipeline for High-Throughput SNP Target Extraction

gwas2crispr 0.1.2

• CLI improvements: The command-line script (inst/scripts/gwas2crispr.R) no longer forces file output. The --out/-o option is now truly optional: omit it to run the pipeline in memory without writing any files. A new --verbose/-v flag prints a concise summary when no outputs are written. The double comma in the option definition has been fixed.
• Console output: All side‑effects (print()/cat()) have been replaced with message() behind a verbose flag. By default, functions run quietly unless verbose = TRUE or the new CLI flag is used.
• Testing: Added tests/testthat/test-run_gwas2crispr.R to ensure that run_gwas2crispr() writes only to a provided out_prefix and returns objects without writing by default.
• Documentation: Updated DESCRIPTION with expanded acronyms and method references; ensured Language: en-US and valid Bioconductor biocViews. Updated the README and vignette to reflect the new no-default-write behaviour and optional CLI output. Added a simple inst/CITATION entry. Bumped version to 0.1.2.

gwas2crispr 0.1.1

• Address CRAN review:
• Expanded acronyms in DESCRIPTION (GWAS, EFO, SNP, BED, FASTA, CRISPR).
• Added method reference: Sudlow et al. (2015) .
• Replaced \dontrun{} with \donttest{} where network I/O may occur; kept other examples short.
• No default file writing: run_gwas2crispr(out_prefix = NULL) now returns objects only.
• Examples/vignette/tests write only to tempdir() when needed.
• Console output is suppressible via verbose + message(); removed cat()/print() side-effects.
• Qualified utils::capture.output to avoid NOTES.
• Vignette updated: object-only example by default; optional tempdir() example for file outputs.
• Fixed CLI script: corrected --out option to use type = "character".
• Fixed CITATION: defined meta object before using meta$Version.
• Corrected Language field and expanded Description with acronym explanations and references.

gwas2crispr 0.1.0

• Initial public release.
• Fetch GWAS associations and export CSV/BED/FASTA for GRCh38/hg38.
• CLI script at inst/scripts/gwas2crispr.R.

gwas2crispr documentation built on Aug. 23, 2025, 1:12 a.m.