Package: seqmagick
Title: Sequence Manipulation Utilities
Version: 0.1.9
Authors@R: c(
    person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6485-8781"))
    )
Description: Tools for reading and writing biological sequences in
        multiple formats, including 'FASTA', 'PHYLIP', 'CLUSTAL',
        'STOCKHOLM', 'MEGA' and 'GenBank'. Supports interleaved and
        sequential layouts where applicable, and reads or writes gzip,
        bzip2 and xz compressed files transparently. Converts between
        formats, renames sequences via a two-column mapping, summarizes
        sequence counts, lengths, GC content and ambiguous characters,
        and manipulates sequence sets (e.g., filtering by patterns and
        computing consensus sequences from alignments). Also includes
        functions to download nucleotide records from NCBI by
        accession.
Depends: R (>= 4.1.0)
Imports: Biostrings, stats, utils, yulab.utils (>= 0.2.5)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), GenomicAlignments,
        GenomicRanges, IRanges, muscle, Rsamtools, prettydoc
VignetteBuilder: knitr
ByteCompile: true
URL: https://github.com/YuLab-SMU/seqmagick
BugReports: https://github.com/YuLab-SMU/seqmagick/issues
License: Artistic-2.0
Encoding: UTF-8
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake make libuv1-dev zlib1g-dev
Repository: https://yulab-smu.r-universe.dev
Date/Publication: 2026-08-29 16:36:48 UTC
RemoteUrl: https://github.com/yulab-smu/seqmagick
RemoteRef: HEAD
RemoteSha: 17f392cbd7e1690ca85ad4783cb7ababfe2eb556
NeedsCompilation: no
Packaged: 2026-10-09 11:40:36 UTC; root
Author: Guangchuang Yu [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>