Type: Package
Package: orthos
Title: `orthos` is an R package for variance decomposition using
        conditional variational auto-encoders
Version: 1.7.2
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, 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
RoxygenNote: 7.3.2
StagedInstall: no
git_url: https://git.bioconductor.org/packages/orthos
git_branch: devel
git_last_commit: 6fddb26
git_last_commit_date: 2025-06-04
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-05 01:12:32 UTC; biocbuild
Author: Panagiotis Papasaikas [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-1640-7636>),
  Charlotte Soneson [aut] (ORCID:
    <https://orcid.org/0000-0003-3833-2169>),
  Michael Stadler [aut] (ORCID: <https://orcid.org/0000-0002-2269-4934>),
  Friedrich Miescher Institute for Biomedical Research [cph]
Maintainer: Panagiotis Papasaikas <panagiotis.papasaikas@fmi.ch>
Built: R 4.5.0; ; 2025-06-05 13:36:32 UTC; windows
