seahtrue
This is thereleased version of seahtrue; for the devel version, seeseahtrue.
Seahtrue revives XF data for structured data analysis
Bioconductor version: Release (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("seahtrue")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("seahtrue")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("seahtrue")| Introduction to Seahtrue | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect,CellBasedAssays,CellBiology,Cheminformatics,DataImport,DataRepresentation,ExperimentalDesign,FunctionalPrediction,GO,Metabolomics,MicrotitrePlateAssay,Preprocessing,QualityControl,Software,Visualization |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (1 year) |
| 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
| Suggests | rmarkdown,knitr,testthat (>= 3.0.0),BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | seahtrue_1.4.0.tar.gz |
| Windows Binary (x86_64) | seahtrue_1.4.0.zip (64-bit only) |
| macOS Binary (x86_64) | seahtrue_1.4.0.tgz |
| macOS Binary (arm64) | seahtrue_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/seahtrue |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/seahtrue |
| Bioc Package Browser | https://code.bioconductor.org/browse/seahtrue/ |
| Package Short Url | https://bioconductor.org/packages/seahtrue/ |
| Package Downloads Report | Download Stats |