Package: tantale
Title: Mining and Analysis of Transcription Activator-Like Effectors
Version: 0.99.0.9000
Authors@R: c(
    person(given = c("Bao", "Tram"), family ="Vi",
    email = "vbt576@gmail.com", role = c("aut"),
    comment = c(ORCID = "0000-0002-4319-5544")),
    person(given = "Sebastien", family = "Cunnac",
    email = "sebastien.cunnac@ird.fr", role = c("aut", "cre"),
    comment = c(ORCID = "0000-0002-3695-491X")),
    person(given = c("Alvaro", "L."), family = "Pérez-Quintero",
    role = "cph",
    comment = "Author of the bundled TALVEZ 3.2 and of the FuncTAL table behind rvd_dna_specificity"),
    person(given = "Molly", family = "Megraw", role = "cph",
    comment = "Author of the PlantTFBS Java classes bundled with TALVEZ (simplescancode/)"),
    person(given = c("Artemis", "G."), family = "Hatzigeorgiou", role = "cph",
    comment = "Author of the PlantTFBS Java classes bundled with TALVEZ (simplescancode/)")
          )
Maintainer: Sebastien Cunnac <sebastien.cunnac@ird.fr>
Description: A toolkit for the study of transcription activator-like
        effectors (TALEs) of Xanthomonas. tell_tales() finds TALE genes
        in genome assemblies and can correct the frameshifts that make
        them hard to annotate in error-prone long-read assemblies.
        TALEs are held in S3 classes that record each one as a series
        of parts (N-terminus, repeats with their repeat-variable
        diresidues (RVDs), C-terminus), with methods to validate,
        subset, combine and plot them. TALEs are aligned repeat by
        repeat, compared with R implementations of the 'DisTAL' and
        'FuncTAL' distances <doi:10.3389/fpls.2015.00545>, and grouped
        into families by hierarchical clustering or k-medoids. Wrappers
        for 'AnnoTALE' <doi:10.1038/srep21077>, 'TALEcorrection'
        <doi:10.1186/s12864-023-09228-1>, 'TALVEZ'
        <doi:10.1371/journal.pone.0068464> and 'PrediTALE'
        <doi:10.1371/journal.pcbi.1007206> read their results into the
        same objects; the last two predict target sites in host
        genomes.
License: MIT + file LICENSE
Copyright: tantale authors, except the bundled third-party programs and
        data listed with their licences in inst/COPYRIGHTS
URL: https://scunnac.github.io/tantale/,
        https://github.com/scunnac/tantale
BugReports: https://github.com/scunnac/tantale/issues
Depends: R (>= 4.0.0)
SystemRequirements: Java (>= 8), and conda, mamba or micromamba (which
        tantale_setup() uses to install MAFFT, HMMER and MMseqs2)
Imports: magrittr, fs, dplyr, ggplot2 (>= 3.5.0), tibble, stringr,
        readr, glue, IRanges, Biostrings, pwalign, GenomicRanges,
        BSgenome, plyranges, systemPipeR, DECIPHER, ape, ggtree,
        tidytree, aplot, universalmotif, gplots, cluster, ggnewscale,
        matrixStats, reticulate, cli, digest, methods, rlang, tidyr,
        stats, utils, grDevices, graphics, BiocGenerics, BiocParallel,
        GenomeInfoDb, S4Vectors, rtracklayer
Suggests: knitr, DT, sessioninfo, biomartr, rmarkdown, quarto, covr,
        testthat (>= 3.0.0), withr, codetools
VignetteBuilder: quarto
Config/Needs/website: pkgdown, tidyverse/tidytemplate
Config/testthat/edition: 3
Config/testthat/parallel: false
Encoding: UTF-8
OS_type: unix
biocViews: Software
Config/roxygen2/version: 8.0.0
Roxygen: list(markdown = TRUE)
LazyData: true
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev make default-jdk libbz2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev
        libssl-dev python3 libx11-dev xz-utils zlib1g-dev
Repository: https://ropensci-staging.r-universe.dev
Date/Publication: 2026-10-09 12:48:37 UTC
RemoteUrl: https://github.com/scunnac/tantale
RemoteRef: HEAD
RemoteSha: 398c06635a747806ebb0337f9f1198a4a2221462
NeedsCompilation: no
Packaged: 2026-10-09 16:33:04 UTC; root
Author: Bao Tram Vi [aut] (ORCID: <https://orcid.org/0000-0002-4319-5544>),
  Sebastien Cunnac [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3695-491X>),
  Alvaro L. Pérez-Quintero [cph] (Author of the bundled TALVEZ 3.2 and of
    the FuncTAL table behind rvd_dna_specificity),
  Molly Megraw [cph] (Author of the PlantTFBS Java classes bundled with
    TALVEZ (simplescancode/)),
  Artemis G. Hatzigeorgiou [cph] (Author of the PlantTFBS Java classes
    bundled with TALVEZ (simplescancode/))