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Bioconductor - seahtrue (development version)

seahtrue

This is the development version of seahtrue; for the stable release version, see seahtrue.

Seahtrue revives XF data for structured data analysis

Bioconductor version: Development (3.22)

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.

Author: Vincent de Boer [cre, aut] ORCID: 0000-0001-9928-1698 , Gerwin Smits [aut], Xiang Zhang [aut]

Maintainer: Vincent de Boer <vincent.deboer at wur.nl>

Citation (from within R, enter citation("seahtrue")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("seahtrue")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("seahtrue")

Details biocViews BatchEffect, CellBasedAssays, CellBiology, Cheminformatics, DataImport, DataRepresentation, ExperimentalDesign, FunctionalPrediction, GO, Metabolomics, MicrotitrePlateAssay, Preprocessing, QualityControl, Software, Visualization Version 1.3.0 In Bioconductor since BioC 3.20 (R-4.4) (0.5 years) License Artistic-2.0 Depends R (>= 4.2.0) 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) System Requirements URL https://vcjdeboer.github.io/seahtrue/ Bug Reports https://vcjdeboer.github.io/seahtrue/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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