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
NeedsCompilation: no
Packaged: 2026-08-30 06:12:08 UTC; wang
Author: Guangchuang Yu [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Repository: CRAN
Date/Publication: 2026-08-30 06:30:02 UTC
