bioc-issue-bot
commented
5 months ago Hi @phauchamps
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: CytoMDS
Title: Low Dimensions projection of cytometry samples
Version: 0.99.8
Authors@R:
c(person(given = "Philippe",
family = "Hauchamps",
role = c("aut", "cre"),
email = "philippe.hauchamps@uclouvain.be",
comment = c(ORCID = "0000-0003-2865-1852")),
person(given = "Laurent", family = "Gatto",
email = "laurent.gatto@uclouvain.be",
role = "aut",
comment = c(ORCID = "0000-0002-1520-2268")),
person(given = "Dan",
family = "Lin",
role = "ctb",
email = "dan.8.lin@gsk.com"))
Description: This package implements a low dimensional visualization of a set
of cytometry samples, in order to visually assess the 'distances' between them.
This, in turn, can greatly help the user to identify quality issues
like batch effects or outlier samples, and/or check the presence of potential
sample clusters that might align with the exeprimental design.
The CytoMDS algorithm combines, on the one hand, the concept of Earth Mover's
Distance (EMD), a.k.a. Wasserstein metric and, on the other hand,
the Multi Dimensional Scaling (MDS) algorithm for the low dimensional
projection.
Also, the package provides some diagnostic tools for both checking the quality
of the MDS projection, as well as tools to help with the interpretation of
the axes of the projection.
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
BugReports: https://github.com/UCLouvain-CBIO/CytoMDS/issues
URL: https://uclouvain-cbio.github.io/CytoMDS
biocViews: FlowCytometry, QualityControl, DimensionReduction,
MultidimensionalScaling, Software, Visualization
Collate:
'CytoMDS.R'
'stats.R'
'ggplots.R'
Depends:
R (>= 4.3)
Imports:
stats,
rlang,
pracma,
withr,
methods,
flowCore,
ggplot2,
ggrepel,
ggforce,
patchwork,
transport,
smacof,
BiocParallel,
CytoPipeline
Suggests:
testthat (>= 3.0.0),
vdiffr,
diffviewer,
knitr,
rmarkdown,
BiocStyle
VignetteBuilder: knitr
Config/testthat/edition: 3
phauchamps
DarioS
lshep
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