README.md

Single Cell TK

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Installation

Release Version

You can download the release version of the Single Cell Toolkit in Bioconductor v3.7:

if (!requireNamespace("BiocManager", quietly=TRUE))
  install.packages("BiocManager")
BiocManager::install("singleCellTK")

Devel Version

You can download the development version of the Single Cell Toolkit in Bioconductor v3.8 or from this repository:

# install.packages("devtools")
devtools::install_github("compbiomed/singleCellTK")

R 3.4 Version

If you are still running an earlier version of R instead of 3.5, you can install the following version from this repository:

# install.packages("devtools")
devtools::install_github("compbiomed/singleCellTK", ref="r_3_4")

Troubleshooting Installation

For the majority of users, the commands above will install the latest version of the singleCellTK without any errors. Rarely, you may encounter an error due to previously installed versions of some packages that are required for the singleCellTK. If you encounter an error during installation, use the commands below to check the version of Bioconductor that is installed:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::version()

If the version number is not 3.6 or higher, you must upgrade Bioconductor to install the toolkit:

BiocManager::install()

After you install Bioconductor 3.6 or higher, you should be able to install the toolkit using devtools::install_github("compbiomed/singleCellTK"). If you still encounter an error, ensure your Bioconductor packages are up to date by running the following command.

BiocManager::valid()

If the command above does not return TRUE, run the following command to update your R packages:

BiocManager::install()

Then, try to install the toolkit again:

devtools::install_github("compbiomed/singleCellTK")

If you still encounter an error, please contact us and we'd be happy to help.

Develop singleCellTK

To contribute to singleCellTK, follow these steps:

Note: singleCellTK is developed to eventually be added to bioconductor. The current version of bioconductor works best with R >= 3.3.1

  1. Fork the repo using the "Fork" button above.
  2. Download a local copy of your forked repository "git clone https://github.com/{username}/singleCellTK.git"
  3. Open Rstudio
  4. Go to "File" -> "New Project" -> "Existing Directory" and select your git repository directory

You can then make your changes and test your code using the Rstudio build tools. There is a lot of information about building packages available here: http://r-pkgs.had.co.nz/.

Information about building shiny packages is available here: http://shiny.rstudio.com/tutorial/.

When you are ready to upload your changes, commit them locally, push them to your forked repo, and make a pull request to the compbiomed repository.

Report bugs and request features on our GitHub issue tracker.

Join us on slack!



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singleCellTK documentation built on Dec. 2, 2018, 6 p.m.