Seahtrue overview | Extracellular flux analysis scientific primer | Resources | Seahtrue | Inspect the seahtrue data | Rate data | Raw data | Assay info | Injection info | Session info
Package: seahtrue 1.7.0
Vincent de Boer
seahtrue: Seahtrue revives XF data for structured data analysis
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.
Authors:
seahtrue_1.7.0.tar.gz
seahtrue_1.7.0.zip(r-4.7)seahtrue_1.7.0.zip(r-4.6)seahtrue_1.7.0.zip(r-4.5)
seahtrue_1.7.0.tgz(r-4.6-any)seahtrue_1.7.0.tgz(r-4.5-any)
seahtrue_1.7.0.tar.gz(r-4.7-any)seahtrue_1.7.0.tar.gz(r-4.6-any)
seahtrue_1.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
seahtrue/json (API)
| # Install 'seahtrue' in R: |
| install.packages('seahtrue', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/vcjdeboer/seahtrue/issues
Datasets:
- revive_output_donor_A - Dataset PBMC donor A
On BioConductor:seahtrue-1.7.0(bioc 3.24)seahtrue-1.6.0(bioc 3.23)
cellbasedassaysfunctionalpredictiondatarepresentationdataimportcellbiologycheminformaticsmetabolomicsmicrotitreplateassayvisualizationqualitycontrolbatcheffectexperimentaldesignpreprocessinggo
Last updated from:98febcffc1. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 166 | ||
| linux-devel-x86_64 | OK | 379 | ||
| source / vignettes | OK | 409 | ||
| linux-release-x86_64 | OK | 349 | ||
| macos-release-arm64 | OK | 170 | ||
| macos-oldrel-arm64 | OK | 169 | ||
| windows-devel | OK | 317 | ||
| windows-release | OK | 333 | ||
| windows-oldrel | OK | 301 | ||
| wasm-release | OK | 146 |
Exports:glue_xfplatesrevive_xfplatesketch_assimilate_ratesketch_assimilate_rawsketch_platesketch_rate
Dependencies:bitbit64cellrangerclicliprcolorspacecpp11crayondplyrfarverforcatsgenericsggplot2ggridgesgluegtablehmsisobandjanitorlabelinglifecycleloggerlubridatemagrittrpillarpitonpkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppreadrreadxlrematchrlangS7scalessettingssnakecasestringistringrtibbletidyrtidyselecttidyxltimechangetzdbutf8validatevctrsviridisLitevroomwithryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Glueing mulltiple plates from a folder | glue_xfplates |
| Dataset PBMC donor A | revive_output_donor_A |
| Running the read, preprocess and validate | revive_xfplate |
| Combine multiple revived xf plates into one plot for rate data | sketch_assimilate_rate |
| Combine multiple revived xf plates into one plot for raw data | sketch_assimilate_raw |
| Make an overview of plate layout, with colored groups | sketch_plate |
| Generate a plot for the rate data | sketch_rate |
