DESCRIPTION

Package: inferrnal
Title: Interface to Call Programs from Infernal RNA Covariance Model Package
Version: 0.99.9
Authors@R: 
    person(given = "Brendan",
           family = "Furneaux",
           role = c("aut", "cre"),
           email = "brendan.furneaux@gmail.com",
           comment = c(ORCID = "0000-0003-3522-7363"))
Description: Search for matches to a covariance model in RNA sequences, or
    align RNA sequences to a covariance model. Covariance models use a
    combination of primary structure (nucleotide sequence) and secondary
    structure (base pairing) to model non-protein-coding RNA families.
    This package is a thin wrapper around the Infernal package, which is not
    included and needs to be installed independently. Functions to read,
    write, and manipulate multiple sequence alignments in Stockholm
    format are also included.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: FALSE
SystemRequirements: Infernal
URL: https://github.com/brendanf/inferrnal
BugReports: https://github.com/brendanf/inferrnal/issues
Imports: 
    assertthat,
    Biostrings,
    IRanges,
    methods,
    stats,
    utils
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
biocViews:
    SequenceMatching,
    ThirdPartyClient,
    Metagenomics,
    HiddenMarkovModel,
    DNASeq,
    RNASeq,
    Annotation,
    Alignment,
    MultipleSequenceAlignment
Suggests: 
    testthat (>= 3.0.0),
    knitr,
    rmarkdown,
    covr,
    ShortRead
VignetteBuilder: knitr
Config/testthat/edition: 3