simpleSeg

DOI: 10.18129/B9.bioc.simpleSeg  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see simpleSeg.

A package to perform simple cell segmentation

Bioconductor version: 3.17

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.

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

Maintainer: Ellis Patrick <ellis.patrick at sydney.edu.au>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("simpleSeg")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("simpleSeg")

 

HTML	R Script	Introduction to simpleSeg
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, Normalization, SingleCell, Software, Spatial, Survival
Version	1.2.5
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
License	GPL-3
Depends	R (>= 3.5.0)
Imports	BiocParallel, EBImage, terra, stats, spatstat.geom, S4Vectors, grDevices, SummarizedExperiment, methods, cytomapper
LinkingTo
Suggests	BiocStyle, testthat (>= 3.0.0), knitr, ggplot2
SystemRequirements
Enhances
URL	https://sydneybiox.github.io/simpleSeg/ https://github.com/SydneyBioX/simpleSeg
BugReports	https://github.com/SydneyBioX/simpleSeg/issues
Depends On Me
Imports Me
Suggests Me	spicyWorkflow
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	simpleSeg_1.2.5.tar.gz
Windows Binary	simpleSeg_1.2.5.zip
macOS Binary (x86_64)	simpleSeg_1.2.5.tgz
macOS Binary (arm64)	simpleSeg_1.2.5.tgz
Source Repository	git clone https://git.bioconductor.org/packages/simpleSeg
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/simpleSeg
Bioc Package Browser	https://code.bioconductor.org/browse/simpleSeg/
Package Short Url	https://bioconductor.org/packages/simpleSeg/
Package Downloads Report	Download Stats