NB This package is no longer being developed. Please check out our package cytobox, which builds and improves cytokit functionality.

cytokit: README

Kleinman Lab toolkit for analyzing single cell RNA-seq data.

Installation

You will need to install devtools, and then run:

devtools::install_github("sjessa/cytokit", build_vignettes = TRUE)

Getting help

Access the barebones vignette from within R for a list of examples:

browseVignettes("cytokit")

You can look up the documentation for any cytokit function from the R console, these also contain an example or two for many functions:

?cytokit::tsne

Some functions will specify the author in the documentation, whom you could contact directly :)

Versioning

Semantic versioning

cytokit uses a semantic versioning scheme, where package versions are of the form x.y.z:

• The patch version z is updated for very minor changes like bug fixes
• The minor version y is udpated for minor but important changes like addition of new functions
• The major version x is updated for major changes, which may introduce backwards incompatibiility

Keeping track of cytokit versions in your work

If you use R Markdown, it's a great idea to include the following function as the last chunk in your documents, which will print a list of all packages loaded, and their versions.

sessionInfo()

If you work with scripts, you could print the following to STDOUT/the log files:

packageVersion("cytokit")

Contribution

The first time

Clone the repository and create a development branch:

git clone https://github.com/sjessa/cytokit.git
cd cytokit
git checkout -b dev-selin

Make changes locally on your branch and once the package passes R CMD check with 0 errors, commit them. Then, push your changes:

git push -u origin dev-selin

If the Travis build passes, there will be a green checkmark next to the most recent commit on your branch. When the build has passed, create a pull request on the GitHub website and merge changes in your dev branch with the master branch.

From now on

From now on, to continue contributing to the package, switch to your branch and make your changes there, following the same edit/commit/push workflow.

If changes have been made to master since first merge the latest changes from the master branch:

git checkout master
git pull
git checkout dev-selin
# Apply all the changes from master to dev-selin, and set HEAD so that new work
# will happen on top of those changes
git rebase master

For more on rebasing, see: https://www.atlassian.com/git/tutorials/merging-vs-rebasing