RUCova

[astaburuaga-garcia]

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• Repository: https://github.com/molsysbio/RUCova

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[bioc-issue-bot]

Hi @astaburuaga-garcia

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: RUCova
Title: Removes unwanted covariance from mass cytometry data 
Version: 0.99.0
Authors@R: person("Rosario", "Astaburuaga-García", , "rosario.astaburuaga@charite.de", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1179-4080"))
Description: Mass cytometry data is high dimensional and contains unwanted covariance induced by variations in cell size, staining and other technical artefacts. This package uses a set of linear models to model and remove unwanted covariance from this data.   
License: use_gpl3_license()
Encoding: UTF-8
biocViews: Software, SingleCell
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Suggests: 
    knitr,
    rmarkdown,
    BiocManager
Imports:
    dplyr,
    tidyr,
    fastDummies,
    ggcorrplot,
    ggh4x,
    ggplot2,
    ggpubr,
    ggridges,
    stringr,
    tibble,
    Matrix,
    ComplexHeatmap,
    grid,
    remotes,
    circlize,
VignetteBuilder: knitr
Depends: 
    R (>= 2.10)
LazyData: true

[lshep]

Please update you DESCRIPTION for a valid license field.

You mention mass cytometry but I don't see an integration with our common
Bioconductor class for this data Spectra. Please provide interoperability with
this class.

Please remove commented out sections of vignette

[astaburuaga-garcia]

Please update you DESCRIPTION for a valid license field.

Updated.

You mention mass cytometry but I don't see an integration with our common Bioconductor class for this data Spectra. Please provide interoperability with this class.

Our package works for mass cytometry data, not mass spectrometry (Spectra).

Please remove commented out sections of vignette

Done

[lshep]

It still seems like this could interact with common Bioconductor classes like a SummarizedExperiment and flowSet? You can see HDCytoData for reference

[lshep]

May we expect any updates soon?

[astaburuaga-garcia]

Hi, yes. Sorry for the delay. I'm adapting the whole pipeline to interact with a SingleCellExperiment class. I'll write here as soon as it is implemented and in the devel branch.

[astaburuaga-garcia]

Hi! I updated the functions and vignette so the workflow interacts with a SingleCellExperiment. The new implementation is on the devel branch.