Package: CRISPRseek
Type: Package
Title: Design of target-specific guide RNAs in CRISPR-Cas9,
        genome-editing systems
Version: 1.40.0
Date: 2022-06-21
Encoding: UTF-8
Author: Lihua Julie Zhu, Paul Scemama, Benjamin R. Holmes, Hervé Pagès, Kai Hu, Hui Mao, Michael Lawrence, Isana Veksler-Lublinsky, Victor Ambros, Neil Aronin and Michael Brodsky
Maintainer: Lihua Julie Zhu <julie.zhu@umassmed.edu>
Depends: R (>= 3.5.0), BiocGenerics, Biostrings
Imports: parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges,
        BSgenome, hash, methods,reticulate,rhdf5,XVector, DelayedArray,
        GenomeInfoDb, GenomicRanges, dplyr, keras, mltools
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, testthat
Description: The package includes functions to find potential guide RNAs for the CRISPR editing system including Base Editors and the Prime Editor for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. The package also output indels and their frequencies for Cas9 targeted sites.
License: GPL (>= 2)
biocViews: ImmunoOncology, GeneRegulation, SequenceMatching, CRISPR
RoxygenNote: 7.1.2
NeedsCompilation: no
git_url: https://git.bioconductor.org/packages/CRISPRseek
git_branch: RELEASE_3_17
git_last_commit: 9be9a24
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-25
Packaged: 2023-04-25 20:46:05 UTC; biocbuild
Built: R 4.3.1; ; 2023-08-25 20:28:55 UTC; unix
