DESCRIPTION

Package: seahtrue
Type: Package
Title: Seahtrue revives XF data for structured data analysis
Version: 0.99.3
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)
Remotes: bioc::BiocStyle
RoxygenNote: 7.3.1
Depends:
    R (>= 4.2.0) 
VignetteBuilder: knitr
URL: https://vcjdeboer.github.io/seahtrue/
BugReports: https://vcjdeboer.github.io/seahtrue/issues