Type: Package
Package: MetaScope
Title: Tools and functions for preprocessing 16S and metagenomic
        sequencing microbiome data
Version: 2.0.0
Authors@R: c(
    person("Sean", "Lu", , "seanlu96@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0009-0007-8005-6125")),
    person("Aubrey", "Odom", , "aodom@bu.edu", role = c("aut"),
           comment = c(ORCID = "0000-0001-7113-7598")),
    person("Rahul", "Varki", , "rvarki@bu.edu", role = "aut",
           comment = c(ORCID = "0009-0003-5721-9484")),
    person("W. Evan", "Johnson", , "wej@bu.edu", role = "aut",
           comment = c(ORCID = "0000-0002-6247-6595"))
  )
Description: This package contains tools and methods for preprocessing
        microbiome data. Functionality includes library generation,
        demultiplexing, alignment, and microbe identification.  It is
        in part an R translation of the PathoScope 2.0 pipeline.
License: GPL (>= 3)
URL: https://github.com/wejlab/metascope
        https://wejlab.github.io/metascope-docs/
BugReports: https://github.com/wejlab/MetaScope/issues
Depends: R (>= 4.2.0)
Imports: BiocFileCache, Biostrings, data.table (>= 1.16.2), dplyr,
        ggplot2, magrittr, Matrix, MultiAssayExperiment, purrr,
        Rbowtie2, readr, rlang, Rsamtools, S4Vectors, stringr,
        SummarizedExperiment, taxonomizr, tibble, tidyr, tools
Suggests: animalcules, BiocStyle, biomformat, GenomicRanges, IRanges,
        knitr, lintr, plyr, R.utils, RCurl, rmarkdown, Rsubread,
        spelling, sys, testthat, usethis
Enhances: BiocParallel
VignetteBuilder: knitr
BiocType: Software
biocViews: MicrobiomeData, ReproducibleResearch, SequencingData
Encoding: UTF-8
Language: en-US
LazyData: FALSE
RoxygenNote: 7.3.3
Config/pak/sysreqs: libbz2-dev libicu-dev liblzma-dev libssl-dev
        libx11-dev xz-utils zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28 12:36:34 UTC
RemoteUrl: https://github.com/bioc/MetaScope
RemoteRef: RELEASE_3_23
RemoteSha: 1f2155fa3662f840fac427b934234f2065e5f0b8
NeedsCompilation: no
Packaged: 2026-10-10 11:21:19 UTC; root
Author: Sean Lu [aut, cre] (ORCID: <https://orcid.org/0009-0007-8005-6125>),
  Aubrey Odom [aut] (ORCID: <https://orcid.org/0000-0001-7113-7598>),
  Rahul Varki [aut] (ORCID: <https://orcid.org/0009-0003-5721-9484>),
  W. Evan Johnson [aut] (ORCID: <https://orcid.org/0000-0002-6247-6595>)
Maintainer: Sean Lu <seanlu96@gmail.com>