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


Demo Web Application

10X PBMC Dataset

Analysis walkthroughs

PCA-based basic walkthrough

PCA-based basic walkthrough with pagoda2 web application generation

Pagoda2 Quick analysis

Installation Instructions

To install pagoda2 please follow the instructions below.

System dependencies


Install system dependencies, example here provided for Ubuntu

sudo apt-get update
sudo apt-get -y install build-essential cmake gsl-bin libgsl0-dev libeigen3-dev libboost-all-dev libssl-dev libcurl4-openssl-dev libssl-dev libcairo2-dev libxt-dev libgtk2.0-dev libcairo2-dev xvfb xauth xfonts-base


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 cmake boost eigen gsl 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:


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 X windows system for mac

Go to https://www.xquartz.org/ and follow the instructions for installing the package.

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 /

Install pagoda2 package

Inside R:

# Install Bioconductor dependencies
biocLite(c("GO.db", "org.Hs.eg.db","org.Mm.eg.db", "pcaMethods"), suppressUpdates=TRUE)
install_github("igraph/rigraph") # Don't install with install.packages()

# Install pagoda
# Pagoda2 is now ready to use

Alternative Install padoga2 as a docker container

Please note that the docker container is as of March 2018 not up to date with the main project branch and all the latest features are missing. It is strongly recommended that you install the main release.

Instructions for installing docker container with pagoda2