bioc-issue-bot
commented
3 years ago Hi @nilseling
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: imcRtools
Version: 0.99.0
Title: Methods for imaging mass cytometry data analysis
Description:
This R package supports the handling and analysis of imaging mass cytometry
and other highly multiplexed imaging data. The main functionality includes
reading in single-cell data after image segmentation and measurement, data
formatting to perform channel spillover correction and a number of spatial
analysis approaches. First, cell-cell interactions are detected via spatial
graph construction; these graphs can be visualized with cells representing
nodes and interactions representing edges. Furthermore, per cell, its direct
neighbours are summarized to allow spatial clustering. Per image/grouping
level, interactions between types of cells are counted, averaged and
compared against random permutations. In that way, types of cells that
interact more (attraction) or less (avoidance) frequently than expected by
chance are detected.
Authors@R:
c(person("Nils", "Eling", role = c("aut", "cre"), email = "nils.eling@dqbm.uzh.ch", comment = c(ORCID = "0000-0002-4711-1176")),
person("Tobias", "Hoch", role = "ctb"),
person("Vito", "Zanotelli", role = "ctb"),
person("Jana", "Fischer", role = "ctb"),
person("Daniel", "Schulz", role = "ctb"))
License: GPL-3
Depends:
R (>= 4.1),
SpatialExperiment
Imports:
S4Vectors,
stats,
utils,
SummarizedExperiment,
methods,
pheatmap,
scuttle,
stringr,
readr,
EBImage,
cytomapper,
abind,
BiocParallel,
viridis,
dplyr,
magrittr,
DT,
igraph,
SingleCellExperiment,
vroom,
BiocNeighbors,
RTriangle,
ggraph,
tidygraph,
ggplot2,
data.table
Suggests:
CATALYST,
grid,
tidyr,
BiocStyle,
knitr,
rmarkdown,
markdown,
testthat
biocViews: ImmunoOncology, SingleCell, Spatial, DataImport, Clustering
VignetteBuilder: knitr
URL: https://github.com/BodenmillerGroup/imcRtools
BugReports: https://github.com/BodenmillerGroup/imcRtools/issues
RoxygenNote: 7.1.1
Encoding: UTF-8
nilseling
nturaga
lshep
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