Package: CRMetrics
Title: Cell Ranger Output Filtering and Metrics Visualization
Version: 0.3.3
Authors@R: c(person("Rasmus", "Rydbirk", email = "rrydbirk@bmb.sdu.dk", role = c("aut", "cre")), person("Fabienne", "Kick", email="fabienne.kick@bric.ku.dk", role="aut"), person("Henrietta","Holze", email="henrietta.holze@petermac.org", role="aut"), person("Xian", "Xin", email="xian.xin@bric.ku.dk", role="ctb"), person("Laura", "Wolbeck", email="laura.wolbeck@bric.ku.dk", role="aut"))
Description: Sample and cell filtering as well as visualisation of
        output metrics from 'Cell Ranger' by Grace X.Y. Zheng et al.
        (2017) <doi:10.1038/ncomms14049>. 'CRMetrics' allows for easy
        plotting of output metrics across multiple samples as well as
        comparative plots including statistical assessments of these.
        'CRMetrics' allows for easy removal of ambient RNA using
        'SoupX' by Matthew D Young and Sam Behjati (2020)
        <doi:10.1093/gigascience/giaa151> or 'CellBender' by Stephen J
        Fleming et al. (2022) <doi:10.1101/791699>. Furthermore, it is
        possible to preprocess data using 'Pagoda2' by Nikolas Barkas
        et al. (2021) <https://github.com/kharchenkolab/pagoda2> or
        'Seurat' by Yuhan Hao et al. (2021)
        <doi:10.1016/j.cell.2021.04.048> followed by embedding of cells
        using 'Conos' by Nikolas Barkas et al. (2019)
        <doi:10.1038/s41592-019-0466-z>. Finally, doublets can be
        detected using 'scrublet' by Samuel L. Wolock et al. (2019)
        <doi:10.1016/j.cels.2018.11.005> or 'DoubletDetection' by
        Gayoso et al. (2020) <doi:10.5281/zenodo.2678041>. In the end,
        cells are filtered based on user input for use in downstream
        applications.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.1.0)
biocViews:
Imports: cowplot, dplyr, ggbeeswarm, ggplot2, ggpmisc, ggpubr, ggrepel,
        magrittr, Matrix, methods, R6, scales, sccore,
        sparseMatrixStats, stats, tibble, tidyr, utils
Suggests: conos, data.table, knitr, markdown, pagoda2, reticulate,
        rhdf5, rmarkdown, Seurat, SoupX, testthat (>= 3.0.0)
Roxygen: list(markdown = TRUE)
URL: https://github.com/khodosevichlab/CRMetrics
BugReports: https://github.com/khodosevichlab/CRMetrics/issues
Maintainer: Rasmus Rydbirk <rrydbirk@bmb.sdu.dk>
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libxml2-dev
Repository: https://khodosevichlab.r-universe.dev
Date/Publication: 2026-10-06 12:19:59 UTC
RemoteUrl: https://github.com/khodosevichlab/crmetrics
RemoteRef: HEAD
RemoteSha: 6aa86065fd4205e1923ca86100a00db565171459
NeedsCompilation: no
Packaged: 2026-10-07 09:37:10 UTC; root
Author: Rasmus Rydbirk [aut, cre],
  Fabienne Kick [aut],
  Henrietta Holze [aut],
  Xian Xin [ctb],
  Laura Wolbeck [aut]