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](https://htmlpreview.github.io/?https://github.com/SydneyBioX/simpleSeg/blob/main/vignettes/simpleSeg.html), and integration with further analysis is explained in detail [here](https://github.com/SydneyBioX/spicyWorkflow). Installation -------- Install the package from Bioconductor. ```r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("simpleSeg") ``` Otherwise, install the development version from Github. ```r # 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. * R package related issues should be raised [here](https://github.com/SydneyBioX/simpleSeg/issues). * For general questions and feedback, please contact us directly via [ellis.patrick@sydney.edu.au](mailto:ellis.patrick@sydney.edu.au). ## Author * **Alexander Nicholls** * **Ellis Patrick** - [@TheEllisPatrick](https://twitter.com/TheEllisPatrick) * **Nicolas Canete**