Package: seahtrue
Type: Package
Title: Seahtrue revives XF data for structured data analysis
Version: 1.5.0
Authors@R: c(
          person("Vincent", "de Boer", 
            email = "vincent.deboer@wur.nl", 
            role = c("cre", "aut"),
            comment=c(ORCID="0000-0001-9928-1698")),
          person("Gerwin", "Smits", role = c("aut")),
          person("Xiang", "Zhang", role = c("aut"))
          )
Description: Seahtrue organizes oxygen consumption and extracellular
        acidification analysis data from experiments performed on an XF
        analyzer into structured nested tibbles.This allows for
        detailed processing of raw data and advanced data visualization
        and statistics. Seahtrue introduces an open and reproducible
        way to analyze these XF experiments. It uses file paths to
        .xlsx files. These .xlsx files are supplied by the userand are
        generated by the user in the Wave software from Agilent from
        the assay result files (.asyr). The .xlsx file contains
        different sheets of important data for the experiment; 1. Assay
        Information - Details about how the experiment was set up. 2.
        Rate Data - Information about the OCR and ECAR rates. 3. Raw
        Data - The original raw data collected during the experiment.
        4. Calibration Data - Data related to calibrating the
        instrument. Seahtrue focuses on getting the specific data
        needed for analysis. Once this data is extracted, it is
        prepared for calculations through preprocessing. To make sure
        everything is accurate, both the initial data and the
        preprocessed data go through thorough checks.
biocViews: CellBasedAssays, FunctionalPrediction, DataRepresentation,
        DataImport, CellBiology, Cheminformatics, Metabolomics,
        MicrotitrePlateAssay, Visualization, QualityControl,
        BatchEffect, ExperimentalDesign, Preprocessing, GO
License: Artistic-2.0
Encoding: UTF-8
LazyData: false
Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle
Imports: dplyr (>= 1.1.2), readxl (>= 1.4.1), logger (>= 0.2.2), tidyxl
        (>= 1.0.8), purrr (>= 0.3.5), tidyr (>= 1.3.0), lubridate (>=
        1.8.0), stringr (>= 1.4.1), tibble (>= 3.1.8), validate (>=
        1.1.1), rlang (>= 1.0.0), glue (>= 1.6.2), cli (>= 3.4.1),
        janitor (>= 2.2.0), ggplot2 (>= 3.5.0), RColorBrewer (>=
        1.1.3), colorspace (>= 2.1.0), forcats (>= 1.0.0), ggridges (>=
        0.5.6), readr (>= 2.1.5), scales (>= 1.3.0)
RoxygenNote: 7.3.1
Depends: R (>= 4.2.0)
VignetteBuilder: knitr
URL: https://vcjdeboer.github.io/seahtrue/
BugReports: https://vcjdeboer.github.io/seahtrue/issues
Config/pak/sysreqs: libicu-dev libx11-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:31:24 UTC
RemoteUrl: https://github.com/bioc/seahtrue
RemoteRef: HEAD
RemoteSha: a315884c971905d8d44914b386b1eb1544b8227c
NeedsCompilation: no
Packaged: 2026-03-16 08:00:09 UTC; root
Author: Vincent de Boer [cre, aut] (ORCID:
    <https://orcid.org/0000-0001-9928-1698>),
  Gerwin Smits [aut],
  Xiang Zhang [aut]
Maintainer: Vincent de Boer <vincent.deboer@wur.nl>
Built: R 4.6.0; ; 2026-03-16 08:01:44 UTC; windows
