Package: GUIDEseq
Type: Package
Title: GUIDE-seq and PEtag-seq analysis pipeline
Version: 1.40.0
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
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 14:28:16 UTC
RemoteUrl: https://github.com/bioc/GUIDEseq
RemoteRef: RELEASE_3_22
RemoteSha: 45a0042cc6e397c8a5246c1233d5db6f1b577785
Packaged: 2026-03-08 03:52:45 UTC; root
Built: R 4.5.2; ; 2026-03-08 03:57:14 UTC; windows
