GAMBLR.data

Collection of genomic data for analysis of Mature B-cell neoplasms
Why use GAMBLR.data? How to install? How to use? Release notes GitHub

Install

We recommend installing the package directly from GitHub (requires devtools dependency).

devtools::install_github(
    "morinlab/GAMBLR.data",
    repos = BiocManager::repositories()
)
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Install GAMBLR.data directly from GitHub along with all bundled data.

Quickstart

The quick and easy way to get started is to make sure the devtools dependency is installed, then install the GAMBLR.data and run a simple function that returns metadata to confirm successful setup:

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

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

# Confirm successful setup
get_gambl_metadata() # returns simple metadata data frame
get_coding_ssm() # returns data frame in maf formatting with somatic variants

Installation for developers

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

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

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

setwd("~/GAMBLR.data")

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 packaage (requires the devtools dependency):

devtools::load_all()

GAMBLR.data is a free open-source package, but the Master branch 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.

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