bioc-issue-bot
commented
5 months ago Hi @vcjdeboer
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: seahtrue
Type: Package
Title: Seahtrue revives XF data for structured data analysis
Version: 0.99.0
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,
testthat (>= 3.0.0),
Imports:
dplyr (>= 1.1.2),
readxl (>= 1.4.1),
logger (>= 0.2.2),
tidyxl (>= 1.0.8),
knitr (>= 1.40),
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),
sessioninfo (>= 1.2.2),
details (>= 0.3.0),
knitr (>= 1.46.0)
RoxygenNote: 7.3.1
Depends:
R (>= 4.2.0)
VignetteBuilder: knitr
StagedInstall: no
URL: https://vcjdeboer.github.io/seahtrue/
BugReports: https://vcjdeboer.github.io/seahtrue/issues
lshep
vcjdeboer
hpages
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
Confirm the following by editing each check box to '[x]'
[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
[x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.
[x] I am familiar with the Bioconductor code of conduct and agree to abide by it.
I am familiar with the essential aspects of Bioconductor software management, including:
For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.