Type: Package
Package: orthos
Title: `orthos` is an R package for variance decomposition using
    conditional variational auto-encoders
Version: 1.9.0
Authors@R: c(
    person("Panagiotis", "Papasaikas", , "panagiotis.papasaikas@fmi.ch", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-1640-7636")),
    person("Charlotte", "Soneson", , "charlotte.soneson@fmi.ch", role = "aut",
           comment = c(ORCID = "0000-0003-3833-2169")),
    person("Michael", "Stadler", , "michael.stadler@fmi.ch", role = "aut",
           comment = c(ORCID = "0000-0002-2269-4934")),
    person("Friedrich Miescher Institute for Biomedical Research", role = "cph")
  )
Description: `orthos` decomposes RNA-seq contrasts, for example obtained from a
    gene knock-out or compound treatment experiment, into unspecific and
    experiment-specific components. Original and decomposed contrasts can
    be efficiently queried against a large database of contrasts
    (derived from ARCHS4, https://maayanlab.cloud/archs4/) to identify similar
    experiments. `orthos` furthermore provides plotting functions to visualize
    the results of such a search for similar contrasts.
License: MIT + file LICENSE
Depends:
    R (>= 4.3),
    SummarizedExperiment
Imports:
    AnnotationHub,
    basilisk,
    BiocParallel,
    colorspace,
    cowplot,
    DelayedArray,
    dplyr,
    ExperimentHub,
    ggplot2 (>= 3.4.0),
    ggpubr,
    ggrepel,
    ggsci,
    grDevices,
    grid,
    HDF5Array,
    keras (>= 2.16.0),
    methods,
    orthosData,
    parallel,
    plyr,
    reticulate,
    rlang,
    S4Vectors,
    stats,
    tensorflow,
    tidyr
Suggests: 
    BiocManager,
    BiocStyle,
    htmltools,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
VignetteBuilder: 
    knitr
biocViews: RNASeq, DifferentialExpression, GeneExpression
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.2
StagedInstall: no
git_url: https://git.bioconductor.org/packages/orthos
git_branch: devel
git_last_commit: dc6b128
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
