In EngeLab/CIMseq.publication: The CIMseq.publication package reproduces the figures associated with the CIMseq publication

Release build:

Introduction

Facilitates reproduction of figures associated with the CIM-seq publication.

Prerequisites

Install R, git, and docker first if not installed.

Instructions

In your computers terminal:

1) Clone the repo
git clone https://github.com/EngeLab/CIMseq.publication.git

2) Change to the repo directory
cd CIMseq.publication

3) Get the docker image
docker pull engelab/cim-seq-publication

4) Generate the processed data files
docker run -v $PWD:/home/Github/CIMseq.publication cim-seq-publication Rscript -e "source('./inst/data/data.R'); source('./inst/analysis/runAnalysis.R')"

Figures are located in inst/analysis/name_of_the_analysis/figures.
Counts data for the sorted multiplet dataset and the mouse gut dataset are in the data folder.

Don't forget to clean up the Docker image/container/etc.

EngeLab/CIMseq.publication documentation built on Jan. 29, 2020, 10:03 a.m.