Package: GUIDEseq
Type: Package
Title: GUIDE-seq and PEtag-seq analysis pipeline
Version: 1.39.0
Date: 2024-04-23
Encoding: UTF-8
Author: Lihua Julie Zhu, Michael Lawrence, Ankit Gupta,
       Hervé Pagès , Alper Kucukural, Manuel Garber, Scot A. Wolfe
Maintainer: Lihua Julie Zhu <julie.zhu@umassmed.edu>
Depends: R (>= 3.5.0), GenomicRanges, BiocGenerics
Imports: Biostrings, pwalign, CRISPRseek, ChIPpeakAnno, data.table,
        matrixStats, BSgenome, parallel, IRanges (>= 2.5.5), S4Vectors
        (>= 0.9.6), stringr, multtest, GenomicAlignments (>= 1.7.3),
        GenomeInfoDb, Rsamtools, hash, limma,dplyr, GenomicFeatures,
        rio, tidyr, tools, methods, purrr, ggplot2, openxlsx,
        patchwork, rlang
biocViews: ImmunoOncology, GeneRegulation, Sequencing, WorkflowStep,
        CRISPR
Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
        BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene,
        org.Hs.eg.db, testthat (>= 3.0.0)
VignetteBuilder: knitr
Description: The package implements GUIDE-seq and PEtag-seq analysis workflow
        including functions for filtering UMI and reads with low coverage, obtaining unique insertion 
        sites (proxy of cleavage sites), estimating the locations 
        of the insertion sites, aka, peaks, merging estimated insertion
        sites from plus and minus strand, and performing off target 
        search of the extended regions around insertion sites with mismatches and indels.
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: no
Config/testthat/edition: 3
RoxygenNote: 7.3.1
git_url: https://git.bioconductor.org/packages/GUIDEseq
git_branch: devel
git_last_commit: fc7717b
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
Packaged: 2025-06-04 23:33:35 UTC; biocbuild
Built: R 4.5.0; ; 2025-06-05 13:08:50 UTC; windows
