CellMembrane
An R package with wrappers and pipelines for single cell RNA-seq analysis
Table of Contents
Overview
This package was created to run the Bimber Lab's single-cell RNA-seq pipelines. It primarily provides high-level wrappers around tools (hence the name). The general idea is to facilitate pipelining tools, make those pipelines fault-tolerant across input data, and to provide QC/visualizations when running those pipelines to help interpret results or issues.
Installation
# Make sure to update your Rprofile to include Bioconductor repos, such as adding this line to ~/.Rprofile:
local({options(repos = BiocManager::repositories())})
#Latest version:
devtools::install_github(repo = 'bimberlabinternal/cellmembrane', dependencies = TRUE, upgrade = 'always')Pre-packaged Docker images with all needed dependencies installed can be found on our GitHub Packages page. We recommend using a specific release, which you can do using tags:
docker pull ghcr.io/bimberlabinternal/cellmembrane:latest