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
RoxygenNote: 7.3.2
StagedInstall: no
Config/pak/sysreqs: cmake make libicu-dev libpng-dev libssl-dev python3
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:24:17 UTC
RemoteUrl: https://github.com/bioc/orthos
RemoteRef: HEAD
RemoteSha: dc6b1284fe4fbb08f06d80977ca35e8dd7b870c1
NeedsCompilation: no
Packaged: 2025-11-02 15:42:24 UTC; root
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 4.6.0; ; 2025-11-02 15:45:40 UTC; windows
