scCustomize
Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing
Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing"
scCustomize 
scCustomize is a collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
Vignettes/Tutorials
See accompanying scCustomize website for detailed tutorials of all aspects of scCustomize functionality.
Installing scCustomize
scCustomize can be installed from CRAN on all platforms. For more detailed instructions see Installation.
# Base R
install.packages("scCustomize")
# Using pak
pak::pkg_install("scCustomize")
Release Notes
A full copy of the changes in each version can be found in the NEWS/ChangeLog.
Develop branch
I also maintain a separate development branch* that can be
installed by supplying ref = "develop" in the devtools or remotes
installation command. Version scheme vX.X.X.9yyy.
*Note: While this branch is typically mostly stable it may
contain breaking issues/bugs.
I do try and keep development
ChangeLog
up to date so it’s easier to follow changes than reading commit history.
Bug Reports/New Features
If you run into any issues or bugs please submit a GitHub issue with details of the issue.
- If possible please include a reproducible example (suggest using SeuratData package pbmc dataset for lightweight examples.)
Any requests for new features or enhancements can also be submitted as GitHub issues.
- Even if you don’t know how to implement/incorporate with current package go ahead a submit!
Pull Requests are welcome for bug fixes, new features, or enhancements.
- Please set PR to merge with “develop” branch and provide description of what the PR contains (referencing existing issue(s) if appropriate).