/pagoda2

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

Primary LanguageJavaScriptGNU General Public License v3.0GPL-3.0

Table of Content

Demo Web Application

10X PBMC Dataset

Analysis walkthroughs

Basic Walkthough -- October 2018

PCA-based basic walkthrough

Installation Instructions

Installing pagoda natively

Currently, there is no way to install Pagoda 2 on Windows.

Ubuntu 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

Red-Hat-based distributions Dependencies

Was tested on AWS linux and Centos 7

yum install cairo-devel pango-devel libXt-devel openssl-devel gsl-devel boost-devel libcurl-devel

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 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:

GUI-Installer:

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 devtools
install.packages("devtools")
# Install Bioconductor dependencies
source("http://bioconductor.org/biocLite.R")
biocLite(c("GO.db", "org.Hs.eg.db","org.Mm.eg.db", "pcaMethods"), suppressUpdates=TRUE)
library(devtools)
install_github("igraph/rigraph") # Don't install with install.packages()
install_github("jkrijthe/Rtsne",ref="openmp")
install.packages(c("Cairo","urltools"))

# Install pagoda
install_github("hms-dbmi/pagoda2")
library('pagoda2')
# Pagoda2 is now ready to use

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.