louisfaure / pagoda2

R package for analyzing and interactively exploring large single-cell RNA-seq datasets

Table of Content

• Demo Web Application
• Analysis walkthroughs
• Installation Instructions
  • Installing Mac Dependencies
  • Installing Linux dependencies
  • Installing Pagoda2 as Docker Container

Demo Web Application

10X PBMC Dataset

Analysis walkthroughs

Basic Walkthough -- October 2018

PCA-based basic walkthrough

Installation Instructions

On most linux-based installations, Pagoda should be available simply by running the following code in R console:

install.packages(c("devtools", "BiocManager"))
BiocManager::install(c("AnnotationDbi", "BiocGenerics", "GO.db", "pcaMethods"))
devtools::install_github("hms-dbmi/pagoda2")
library('pagoda2')

If you have Mac, or it doesn't work on your Linux, please see instructions below. Currently, there is no way to install Pagoda 2 on Windows.

Installing Mac Dependencies

You need R >=3.4.0 to install this package on a mac. For installation please refer to cran

You need the homebrew package manager
Run these commands in a terminal:

brew update
brew install curl openssl wget

To enable R to use the parallelized functions in the C++ code, you need another version of the clang++-Compiler for mac.
This is compatible with OS X >= 10.11

Follow these instructions to install clang4 with openmp support:

GUI-Installer:

• Download the clang4-r.pkg (263.6 mb) from https://uofi.box.com/v/r-macos-clang-pkg
  MD5 Hash: f49df42ccc84ec529c489e8e3f02248
• Install it!

Here is a more in depth explanation what is going on and a script to do what the GUI-Installer does by yourself. For Pagoda2 you only need the clang part, not the gfortran part. openmp in r on OS X

Install gfortran for Mac

curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /

Installing Linux dependencies

Installation for Debian-based distributions (e.g. Ubuntu):

sudo apt-get update
sudo apt-get -y install libcurl4-openssl-dev libssl-dev

Installation for Red-Hat-based distributions (e.g. CentOS or Fedora)

yum install openssl-devel libcurl-devel

Installing Pagoda2 as Docker Container

If you are having trouble setting up pagoda2 on your system, an alternative approach to get pagoda on a mac or windows system is through a docker container. The docker distribution is current as of October 2018 and also includes the Conos package. To start a docker container, first install docker on your platform and then start the pagoda container with the following command in the shell:

docker run -p 8787:8787 docker.io/barkasn/pagoda2

The first time you run the command it will download several images so make sure that you have fast internet access setup. You can then point your browser to http://localhost:8787/ to get an Rstudio environment with pagoda2 (and conos) installed (log in using credentials rstudio/pass). Explore the docker --mount option to allow access of the docker image to your local files.