bioc-issue-bot
commented
3 months ago Hi @HsiaoChiLiao
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: MAPFX
Title: MAssively Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for
Analysing Data from the Massively-Parallel Cytometry
Experiments
Version: 0.99.0
Authors@R:
c(person("Hsiao-Chi", "Liao", email = "chelsea.acad@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9586-1246")),
person("Agus", "Salim", role = c("ctb")), person("infinityFlow", role = c("ctb")))
Description: MAPFX is an end-to-end toolbox that pre-processes the raw data from MPC experiments (e.g., BioLegend's LEGENDScreen and BD Lyoplates assays), and further imputes the ‘missing’ infinity markers in the wells without those measurements. The pipeline starts by performing background correction on raw intensities to remove the noise from electronic baseline restoration and fluorescence compensation by adapting a normal-exponential convolution model. Unwanted technical variation, from sources such as well effects, is then removed using a log-normal model with plate, column, and row factors, after which infinity markers are imputed using the informative backbone markers as predictors. The completed dataset can then be used for clustering and other statistical analyses. Additionally, MAPFX can be used to normalise data from FFC assays as well.
Depends: R (>= 4.4.0)
License: GPL-2
Encoding: UTF-8
RoxygenNote: 7.3.1
Roxygen: list(markdown = TRUE)
biocViews: Software, FlowCytometry, CellBasedAssays, SingleCell, Proteomics, Clustering
Imports: flowCore, Biobase, stringr, uwot, iCellR, igraph,
ggplot2, RColorBrewer, Rfast, ggrepel, ComplexHeatmap,
circlize, glmnetUtils, e1071, xgboost, foreach, doParallel,
parallel, pbapply, reshape2, gtools, utils, stats, cowplot, methods, grDevices, graphics
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
URL: https://github.com/HsiaoChiLiao/MAPFX
BugReports: https://github.com/HsiaoChiLiao/MAPFX/issues
lshep
HsiaoChiLiao
jianhong
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.