Package: simpleSeg 1.15.0

Ellis Patrick

simpleSeg: A package to perform simple cell segmentation

Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. This allows for the features of cells such as marker expression and morphology to be extracted, stored and analysed. simpleSeg provides functionality for user friendly, watershed based segmentation on multiplexed cellular images in R based on the intensity of user specified protein marker channels. simpleSeg can also be used for the normalization of single cell data obtained from multiple images.

Authors:Nicolas Canete [aut], Alexander Nicholls [aut], Ellis Patrick [aut, cre]

simpleSeg_1.15.0.tar.gz
simpleSeg_1.15.0.zip(r-4.7)simpleSeg_1.15.0.zip(r-4.6)simpleSeg_1.15.0.zip(r-4.5)
simpleSeg_1.15.0.tgz(r-4.6-any)simpleSeg_1.15.0.tgz(r-4.5-any)
simpleSeg_1.15.0.tar.gz(r-4.7-any)simpleSeg_1.15.0.tar.gz(r-4.6-any)
simpleSeg_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
simpleSeg/json (API)

# Install 'simpleSeg' in R:

install.packages('simpleSeg', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sydneybiox/simpleseg/issues

Pkgdown/docs site:https://sydneybiox.github.io

On BioConductor:simpleSeg-1.15.0(bioc 3.24)simpleSeg-1.14.0(bioc 3.23)

classification survival singlecell normalization spatial spatial-statistics

5.88 score 1 stars 2 packages 25 scripts 502 downloads 2 exports 137 dependencies

Last updated from:446373ed65. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	239
linux-devel-x86_64	OK	555
source / vignettes	OK	391
linux-release-x86_64	OK	542
macos-release-arm64	OK	257
macos-oldrel-arm64	OK	326
windows-devel	OK	493
windows-release	OK	523
windows-oldrel	OK	550
wasm-release	OK	204

Exports:normalizeCells simpleSeg

Dependencies:abind askpass base64enc beeswarm BH Biobase BiocFileCache BiocGenerics biocmake BiocParallel bit bit64 bitops blob bslib cachem cli codetools commonmark cpp11 curl cytomapper DBI dbplyr DelayedArray deldir digest dir.expiry dplyr EBImage evaluate farver fastmap fftwtools filelock fontawesome formatR fs futile.logger futile.options generics GenomicRanges ggbeeswarm ggplot2 glue gridExtra gtable h5mread HDF5Array highr htmltools htmlwidgets httpuv httr2 IRanges isoband jpeg jquerylib jsonlite knitr labeling lambda.r later lattice lifecycle locfit magick magrittr Matrix MatrixGenerics matrixStats memoise mime nnls openssl otel pillar pkgconfig png polyclip promises purrr R6 rappdirs raster RColorBrewer Rcpp RCurl rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown RSQLite S4Arrays S4Vectors S7 sass scales Seqinfo shiny shinydashboard SingleCellExperiment snow sourcetools sp SparseArray SpatialExperiment spatstat.data spatstat.geom spatstat.univar spatstat.utils stringi stringr SummarizedExperiment svglite svgPanZoom sys systemfonts terra textshaping tibble tidyr tidyselect tiff tinytex utf8 vctrs vipor viridis viridisLite withr xfun xtable XVector yaml

Segmenting and normalizing multiplexed imaging data with simpleSeg

Rendered fromsimpleSeg.Rmdusingknitr::rmarkdown

Last update: 2024-05-21
Started: 2022-05-30

Help page	Topics
Utility function to generate BPPARM object.	generateBPParam
Normalizes and transforms cell data in preparation for clustering (accepts dataframe, SingleCellExperiment and SpatialExperiment).	normalizeCells
Perform simple segmentation of multiplexed cellular images	simpleSeg

Package: simpleSeg 1.15.0

simpleSeg: A package to perform simple cell segmentation

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Help Manual

Usage by other packages (reverse dependencies)