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simpleSeg

Overview

simpleSeg provides a structured pipeline for segmentation of cellular tiff stacks and the normalization of features, priming cells for classification / clustering.

A brief preview of simpleSeg can be found here, and integration with further analysis is explained in detail here.

Installation

Install the package from Bioconductor.

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("simpleSeg")

Otherwise, install the development version from Github.

# Install the development version from GitHub:
# install.packages("devtools")
devtools::install_github("SydneyBioX/simpleSeg")
library(simpleSeg)

Installation Problems

Usually caused by non-R dependencies being unavailable. Ensure that the following packages are installed on your system.

fftw, gdal, fortran, arrow

Submitting an issue or feature request

simpleSeg is still under active development. We would greatly appreciate any and all feedback related to the package.

Author