GAMBLR

To be used only by Morin Lab and GAMBL consortium members

Please refer to GAMBLR.open for the open access published version of this package
Why use GAMBLR? How to install? How to use? Release notes GitHub

About

The GAMBLR-verse is a database, mining, manipulation and collection of a convenience functions for working with genomic data of mature B-cell lymphomas. The GAMBLR is an R package that is a wrapper providing a convenient one-stop access to load the following packages from the GAMBLR family:

  • GAMBLR.data - a “storage unit” with different types of bundled data
  • GAMBLR.helpers - a set of low-level functions for data operation
  • GAMBLR.utils - higher level set of functions to operate on genomic data
  • GAMBLR.viz - set of functions used mostly for visualizations
  • GAMBLR.results - collection of functions to efficiently retreive data generated by LCR-modules within GAMBL project
Who should use this package?

This package is for the members of Morin Lab and GAMBL consortium with approved access to the restricted access data. Please refer to GAMBLR.open for the open access published version of this package.

Install

To install this package, we recommend doing it by accessing the latest master version directly from GitHub (requires devtools dependency).

devtools::install_github(
    "morinlab/GAMBLR",
    repos = BiocManager::repositories()
)

Please refer to GAMBLR.open for the open access published version of this package.

This error is because GAMBLR.results package is private and have restricted access. If you are the Moring Lab member or member of the GAMBL consortium, please contact Kostia or Ryan through Slack regarding this error. Be sure your GitHub ID is added to your Slack profile.

Quickstart

The quick and easy way to get started is to make sure the devtools dependency is installed, then install the GAMBLR and run the simplest functions to confirm successful setup:

# Verify devtools is installed
if (!require("devtools")) install.packages("devtools")

# Install GAMBLR
devtools::install_github(
    "morinlab/GAMBLR",
    repos = BiocManager::repositories()
)

We recommend restarting your R session after the installation.

library(GAMBLR)

# Confirm successful setup
metadata <- get_gambl_metadata()
maf <- get_coding_ssm()

Installation for developers

The easiest way to obtain and contribute to GAMBLR is to do this via cloning the repository

cd
git clone git@github.com:morinlab/GAMBLR.git

In your R editor of choice (which is hopefully VS Code), set your working directory to the directory you just cloned the repo into.

setwd("~/GAMBLR")

Install the package in R by running the following command (requires the devtools package):

devtools::install()

After applying your modifications to the code, use the following command to quickly test your changes without directly installing the package (requires the devtools dependency):

devtools::load_all()

The Master branch of the GAMBLR repo is protected. We welcome contributions (pull request, bug report, feature request, PR review) from all levels of users. All commits must be submitted via pull request on a branch. Please refer to the GitHub documentation for details on how to do pull request, or ask for help in the #git-help Slack channel.

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