Package: bcSeq
Type: Package
Title: Fast Sequence Mapping in High-Throughput shRNA and CRISPR
        Screens
Version: 1.35.0
Date: 2019-07-18
Authors@R: c(person("Jiaxing","Lin", role = c("aut", "cre"), 
            email = "jiaxing.lin@duke.edu"), 
            person("Jeremy", "Gresham", role = "aut"),
            person("Jichun", "Xie", role = "aut"),
            person("Kouros", "Owzar", role = "aut"),
            person("Tongrong", "Wang", role = "ctb"),
            person("So Young", "Kim", role = "ctb"),
            person("James", "Alvarez", role = "ctb"),
            person("Jeffrey S.", "Damrauer", role = "ctb"),
            person("Scott", "Floyd", role = "ctb"),
            person("Joshua", "Granek", role = "ctb"),
            person("Andrew", "Allen", role = "ctb"),
            person("Cliburn", "Chan", role = "ctb"))		   	
Author: Jiaxing Lin [aut, cre], Jeremy Gresham [aut], Jichun Xie [aut],
        Kouros Owzar [aut], Tongrong Wang [ctb], So Young Kim [ctb],
        James Alvarez [ctb], Jeffrey S. Damrauer [ctb], Scott Floyd
        [ctb], Joshua Granek [ctb], Andrew Allen [ctb], Cliburn Chan
        [ctb]
Maintainer: Jiaxing Lin <jiaxing.lin@duke.edu>
Description: This Rcpp-based package implements a highly efficient data
        structure and algorithm for performing alignment of short reads
        from CRISPR or shRNA screens to reference barcode library.
        Sequencing error are considered and matching qualities are
        evaluated based on Phred scores. A Bayes' classifier is
        employed to predict the originating barcode of a read. The
        package supports provision of user-defined probability models
        for evaluating matching qualities. The package also supports
        multi-threading.
License: GPL (>= 2)
biocViews: ImmunoOncology, Alignment, CRISPR, Sequencing,
        SequenceMatching, MultipleSequenceAlignment, Software, ATACSeq
URL: https://github.com/jl354/bcSeq
Imports: Rcpp (>= 0.12.12), Matrix, Biostrings
Depends: R (>= 3.4.0)
LinkingTo: Rcpp, Matrix
BugReports: https://support.bioconductor.org
Suggests: knitr
VignetteBuilder: knitr
BuildVignettes: yes
NeedsCompilation: yes
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:46:57 UTC
RemoteUrl: https://github.com/bioc/bcSeq
RemoteRef: HEAD
RemoteSha: 8ba61021631a4b50dc79d6ba66896ef76a9ba348
Packaged: 2026-07-03 13:14:24 UTC; root