Package: conformeR
Type: Package
Title: Conformalized differential expression analysis of
        multi-condition single-cell data
Version: 0.99.1
Authors@R: c(person(given="Justine", family="Leclerc", email="justine.leclerc@usz.ch", role = c("cre", "aut"),
           comment = c(ORCID = "0009-0002-5667-0778")),
    person("Christof", "Seiler", email="christof.seiler@usz.ch", role="aut",
           comment = c(ORCID = "0000-0001-8802-3642")),
    person("Digital Society Initiative - University of Zurich",role = "fnd",
    comment = "RAI - Reliable AI for Biomedicine"))
Description: conformeR provides conformal prediction layers for the
        cell neighborhood construction step of the LEMUR framework. It
        implements two complementary approaches, conformal clustering
        and conformal selection, to quantify uncertainty in the
        resulting cell neighborhoods, together with tools for
        visualizing and interpreting the resulting uncertainty sets.
URL: https://github.com/juslecl/conformeR
BugReports: https://github.com/juslecl/conformeR/issues
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Suggests: testthat (>= 3.0.0), S4Vectors, BiocStyle, tidyr, purrr,
        knitr, rmarkdown, edgeR, MASS, utils
Config/testthat/edition: 3
Imports: dplyr, ggplot2, tibble, SummarizedExperiment,
        SingleCellExperiment, BiocParallel, rsample, rlang, stats,
        lemur, glmGamPoi, uwot, ggnewscale, cowplot, scales, grid,
        methods, tidyselect
Depends: R (>= 4.5.0),
VignetteBuilder: knitr
LazyData: false
BiocType: Software
biocViews: Transcriptomics, DifferentialExpression, SingleCell,
        DimensionReduction, Classification, Clustering,
        Visualization,GeneExpression, GenePrediction, GeneTarget
Config/pak/sysreqs: libicu-dev libssl-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-19 13:54:25 UTC
RemoteUrl: https://github.com/BiocStaging/conformeR
RemoteRef: HEAD
RemoteSha: 87cc23ed1c4c60e8016e6f2d320d8d270009af12
NeedsCompilation: no
Packaged: 2026-10-19 20:13:42 UTC; root
Author: Justine Leclerc [cre, aut] (ORCID:
    <https://orcid.org/0009-0002-5667-0778>),
  Christof Seiler [aut] (ORCID: <https://orcid.org/0000-0001-8802-3642>),
  Digital Society Initiative - University of Zurich [fnd] (RAI - Reliable
    AI for Biomedicine)
Maintainer: Justine Leclerc <justine.leclerc@usz.ch>