Package: CRISPRseek
Version: 1.50.0
Title: Design of guide RNAs in CRISPR genome-editing systems
Author: Lihua Julie Zhu Paul Scemama Benjamin R. Holmes Hervé Pagès Kai
        Hu Hui Mao Michael Lawrence Isana Veksler-Lublinsky Victor
        Ambros Neil Aronin Michael Brodsky Devin M Burris
Maintainer: Lihua Julie Zhu <julie.zhu@umassmed.edu> Kai Hu
 <kai.hu@umassmed.edu>
Date: 2024-11-14
Description: The package encompasses functions to find potential guide
        RNAs for the CRISPR-based genome-editing systems including the
        Base Editors and the Prime Editors when supplied with target
        sequences as input. Users have the flexibility to filter
        resulting guide RNAs based on parameters such as the absence of
        restriction enzyme cut sites or the lack of paired guide RNAs.
        The package also facilitates genome-wide exploration for
        off-targets, offering features to score and rank off-targets,
        retrieve flanking sequences, and indicate whether the hits are
        located within exon regions. All detected guide RNAs are
        annotated with the cumulative scores of the top5 and topN
        off-targets together with the detailed information such as
        mismatch sites and restrictuion enzyme cut sites. The package
        also outputs INDELs and their frequencies for Cas9 targeted
        sites.
Depends: R (>= 3.5.0), BiocGenerics, Biostrings, GenomicFeatures
Imports: parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges,
        BSgenome, hash, methods,reticulate,rhdf5,XVector, DelayedArray,
        Seqinfo, GenomicRanges, dplyr, keras, mltools, gtools,
        openxlsx, rio, rlang, stringr
Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
        TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db,
        BSgenome.Mmusculus.UCSC.mm10,
        TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, lattice,
        MASS, tensorflow, BSgenome.Hsapiens.UCSC.hg38, BiocFileCache,
        TxDb.Hsapiens.UCSC.hg38.knownGene, testthat, knitr
License: file LICENSE
biocViews: ImmunoOncology, GeneRegulation, SequenceMatching, CRISPR
Encoding: UTF-8
RoxygenNote: 7.3.2
NeedsCompilation: no
VignetteBuilder: knitr
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev python3 libx11-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:17:22 UTC
RemoteUrl: https://github.com/bioc/CRISPRseek
RemoteRef: RELEASE_3_22
RemoteSha: fd2babca74a8a1aca65f22410873e597366b80d3
Packaged: 2025-11-11 13:55:56 UTC; root
Built: R 4.5.2; ; 2025-11-11 14:08:48 UTC; windows
