Package: crisprDesign
Title: Comprehensive design of CRISPR gRNAs for nucleases and base
        editors
Version: 1.13.5
Authors@R: c(
    person("Jean-Philippe", "Fortin", email = "fortin946@gmail.com", role = c("aut", "cre")),
    person("Luke", "Hoberecht", email = "lukehob3@gmail.com", role = c("aut"))
    )
Description: 
    Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This 
    includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS
    contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR 
    modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, 
    CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including
    DNA- and RNA-target nucleases such as Cas9, Cas12a, and Cas13d. All types of base editors are
    also supported. gRNA design can be performed on reference genomes, transcriptomes,
    and custom DNA and RNA sequences. Both unpaired and paired gRNA designs are enabled.
Depends: R (>= 4.2.0), crisprBase (>= 1.1.3)
Imports: AnnotationDbi, BiocGenerics, Biostrings (>= 2.77.2), BSgenome
        (>= 1.77.1), crisprBowtie (>= 0.99.8), crisprScore (>= 1.15.2),
        GenomeInfoDb (>= 1.45.7), GenomicFeatures (>= 1.61.4),
        GenomicRanges (>= 1.61.1), IRanges, Matrix, MatrixGenerics,
        methods, reticulate, rtracklayer (>= 1.69.1), S4Vectors,
        Seqinfo, stats, txdbmaker (>= 1.5.6), utils, VariantAnnotation
        (>= 1.55.1)
Suggests: biomaRt, BSgenome.Hsapiens.UCSC.hg38,
        BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa (>= 0.99.7),
        knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat
biocViews: CRISPR, FunctionalGenomics, GeneTarget
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.3
VignetteBuilder: knitr
BugReports: https://github.com/crisprVerse/crisprDesign/issues
URL: https://github.com/crisprVerse/crisprDesign
LazyData: true
git_url: https://git.bioconductor.org/packages/crisprDesign
git_branch: devel
git_last_commit: 3eae211
git_last_commit_date: 2025-11-22
Repository: Bioconductor 3.23
Date/Publication: 2025-11-23
NeedsCompilation: no
Packaged: 2025-11-23 22:05:16 UTC; biocbuild
Author: Jean-Philippe Fortin [aut, cre],
  Luke Hoberecht [aut]
Maintainer: Jean-Philippe Fortin <fortin946@gmail.com>
