bimberlabinternal / oosap

OHSU-ONPRC Single-cell Analysis Package

OOSAP

OHSU-ONPRC Single-cell Analysis Package

The goal of this package is to provide a high-level wrapper around tools and pipelines for the analysis of single-cell RNASeq data.

Table of Contents

• Installation
• Development Guidelines

Installation

# Install requirements.  Other dependencies will be downloaded automatically
install.packages(c('devtools', 'BiocManager', 'remotes'), dependencies=TRUE, ask = FALSE)

# Make sure to update your Rprofile i.e., ~/.Rprofile.site
# local({options(repos = BiocManager::repositories())})

# Get some of the core packages
BiocManager::install(c('org.Hs.eg.db', 'org.Mm.eg.db', 'HSMMSingleCell', 'monocle', 'DelayedMatrixStats', 'DESeq2', 'genefilter'), dependencies=TRUE, ask = FALSE)

#Latest version:
devtools::install_github(repo = 'bimberlabinternal/OOSAP', ref = 'Dev', dependencies = T, upgrade = 'always')

Pre-packaged Docker images with all needed dependencies installed can be found on our GitHub Packages repository:

docker pull ghcr.io/bimberlabinternal/oosap:latest

Development Guidelines

• New development should occur on a branch, and go through a Pull Request before merging into Dev. See here for information on the pull request workflow. Ideally PRs would be reviewed by another person. For the PR, please review the set of changed files carefully to make sure you are only merging the changes you intend.

• New exported functions should have Roxygen2 documentation.

• As part of each PR, you should run 'devtools::document()' to update documentation and include these changes with your commits.

• It is a good idea to run 'R CMD check' locally to make sure your changes will pass. See here for more information

• Code should only be merged after the Travis CI build and tests pass. The Dev branch should always be stable.

• New features should ideally have at least a basic test (see R testthat). There is existing test data in ./tests/testdata. This can be expanded, but please be conscious about file size and try to reuse data across tests if appropriate.