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.
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)Usually caused by non-R dependencies being unavailable. Ensure that the following packages are installed on your system.
fftw, gdal, fortran, arrow
simpleSeg is still under active development. We would greatly appreciate any and
all feedback related to the package.
- R package related issues should be raised here.
- For general questions and feedback, please contact us directly via [email protected].
- Alexander Nicholls
- Ellis Patrick - @TheEllisPatrick
- Nicolas Canete