README.md

In AllenInstitute/CCN: Generate the Standardized Common Cell type Nomenclature (CCN)

CCN

Overview

This repository contains an R library to generate the standardized Common Cell type Nomenclature (CCN) for a cell type taxonomy, and is a companion repository of AllenInstitute/nomenclature. More general information about what the CCN is and why it's important can be found on our website, here, with and updated version now published on eLife.

Specific details of how to apply the CCN to your cell type taxonomy can be found at AllenInstitute/nomenclature or by typing browseVignettes("CCN") in R after installing this library.

Installation

Install prerequisites (if not already installed):

packages <- c("remotes","jsonlite","data.table","ggplot2","dendextend","dplyr","BiocManager")
packages <- packages[!(packages %in% installed.packages()[,"Package"])]
if(length(packages)>0) install.packages(new.packages, repos='http://cran.us.r-project.org')
BiocManager::install("rols", update=FALSE)

Install CCN and its vignettes:

remotes::install_github("AllenInstitute/CCN", build_vignettes = TRUE)

License

The license for this package is available on Github at: https://github.com/AllenInstitute/CCN/blob/master/LICENSE

Level of Support

We are planning on occasional updating this tool with no fixed schedule. Community involvement is encouraged through both issues and pull requests.

Contribution Agreement

If you contribute code to this repository through pull requests or other mechanisms, you are subject to the Allen Institute Contribution Agreement, which is available in full at: https://github.com/AllenInstitute/CCN/blob/master/CONTRIBUTION

AllenInstitute/CCN documentation built on April 15, 2023, 10:48 p.m.