altSEE

The altSEE package contains material and code that extends the iSEE package (https://github.com/iSEE/iSEE).

We welcome contributions from the community, see below for more instructions.

Installation

altSEE can be easily installed from GitHub, you can use:

BiocManager::install("statomics/altSEE", dependencies = TRUE)
# or alternatively...
remotes::install_github("statomics/altSEE", dependencies = TRUE)

Setting dependencies = TRUE should ensure that all packages, including the ones in the Suggests: field of the DESCRIPTION, are installed - this can be essential if you want to reproduce the code in the vignette, for example.

Expanding the iSEE universe with altSEE

• install iSEE first - a forked development version is recommended.

BiocManager::install("statomics/iSEE")
# or
remotes::install_github("statomics/iSEE")

• fork the altSEE repo (https://github.com/statomics/altSEE) and clone it locally.

git clone https://github.com/[your_github_username]/altSEE.git

• make the desired changes in the files - start from the R folder, then document via roxygen2 - and push to your fork.

• once your contribution (function, panel, mode) is done, consider adding some information in the package. Some examples might be a screenshot of the mode in action (to be placed in the folder inst/modes_img), or a well-documented example use case (maybe an entry in the vignettes folder). Also add yourself as a contributor (ctb) to the DESCRIPTION file.

• make a pull request to the original repo - the GitHub site offers a practical framework to do so, enabling comments, code reviews, and other goodies.

• more on documenting and code guidelines:

  • if possible, please consider adding an example in the dedicated Roxygen preamble to show how to run each function
  • if possible, consider adding one or more unit tests - we use the testthat framework