⚠️ The PCAGO and PCAGO-Electon repositories have been merged and are available here:

https://github.com/rnajena/pcago-unified

PCAGO

PCAGO is an interactive web service that allows analysis of RNA-Seq read count data with principal component analysis (PCA) and agglomerative clustering. The tool also includes features like read count normalization, filtering read counts by gene annotation and various visualization options.

PCAGO on GitHub | PCAGO-Electron on GitHub

Running

You have following options to run PCAGO:

• Use our servers (PCAGO Stable or PCAGO Development Version)
• Use a standalone desktop application
• Run the PCAGO server on one of your servers or your local computer

Using the standalone application

Download the PCAGO-Electron here. This application wraps a PCAGO-server within an Electron application.

Running manually

Open a R console in the PCAGO folder and run

shiny::runApp()

**Note: ** If you use packrat (see below), you have to run

source('packrat/init.R')
shiny::runApp()

Requirements

Following packages are required to run PCAGO if the dependencies are already installed:

• R version 3.4.3 (2017-11-30) or higher
• ffmpeg (Debian/Ubuntu: ffmpeg)
• libmariadb (Debian/Ubuntu: libmariadb2)

Following packages are required to install PCAGO if the required libraries have to be installed

• libcurl dev package (Debian/Ubuntu: libcurl4-openssl-dev)
• xml2-config dev package (Debian/Ubuntu: libxml2-dev)
• openssl dev package (Debian/Ubuntu: libssl-dev)
• mariadb dev package (Debian/Ubuntu: libmariadb-client-lgpl-dev)
• cairo2 dev package (Debian/Ubuntu: libcairo2-dev)
• GTK2 dev package (Debian/Ubuntu: libgtk2.0-dev)
• XVFB package (Debian/Ubuntu: xvfb)
• xAuth package (Debian/Ubuntu: xauth)
• xfonts dev package (Debian/Ubuntu: xfonts-baselibgtk2.0-dev)
• xfonts base package (Debian/Ubuntu: xfonts-base)
• libxt dev package (Debian/Ubuntu: libxt-dev)

PCAGO also requires several R packages (see table below). You can either install those packages manually or by using the package management system packrat.

Using packrat

Packrat is a package management system that allows creating snapshots of the libraries used for development of the application. This prevents breakage introduced by newer library versions. To use packrat, follow these steps:

1. Download the package sources
2. Unpack them into the packrat directory within the PCAGO project folder
3. Start R within the project directory
4. Run source('packrat/init.R')

**Important note: ** source('packrat/init.R') must be always called before starting PCAGO to enable packrat. If you want to automate this process or want to deploy a server using Shiny Server, create a file .Rprofile that contains source('packrat/init.R') in the PCAGO directory.

**Important note: ** If the installation of the dependencies failed for any reason source('packrat/init.R') will not continue the installation of the library. Additionally run packrat::restore() to continue the dependency installation.

**Tip: ** You can copy the packrat directory to other computers running the same operating system to skip the building times. This will likely not work if you copy data between different distributions or different versions of the same distribution.

Installing requirements manually

If you do not want to use packrat, you can install the dependencies manually. Please note that newer library versions might break functionality. Following command installs all dependencies:

# CRAN packages
install.packages(c("svglite", "scales", "fastcluster", "gplots", "amap", "dendextend", "VennDiagram", "futile.logger", "plot3D", "scatterplot3d", "ggplot2", "RColorBrewer", "openxlsx", "Cairo", "reshape2", "R6", "matrixStats", "colourpicker", "shinyjs", "shinyBS", "DT", "htmltools", "markdown", "shiny"))

# BioConductor packages. Install them from source, so known bugs with newer R versions can be avoided.
source("https://bioconductor.org/biocLite.R")
biocLite(c("ctc", "GO.db", "GenomicFeatures", "AnnotationDbi", "AnnotationHub", "biomaRt", "rtracklayer", "DESeq2", "SummarizedExperiment", "DelayedArray", "Biobase", "GenomicRanges", "GenomeInfoDb", "IRanges", "S4Vectors", "BiocGenerics"), type = "source")

R packages

Package	Author	URL	License	Version
rmarkdown	JJ Allaire [aut], Yihui Xie [aut, cre] (0000-0003-0645-5666), Jonathan McPherson [aut], Javier Luraschi [aut], Kevin Ushey [aut], Aron Atkins [aut], Hadley Wickham [aut], Joe Cheng [aut], Winston Chang [aut], Jeff Allen [ctb], Roy Storey [ctb], Rob Hyndman [ctb], Ruben Arslan [ctb], RStudio, Inc. [cph], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/rmd/h/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/rmd/h/jqueryui-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), Greg Franko [ctb, cph] (tocify library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library), Dave Gandy [ctb, cph] (Font-Awesome), Ben Sperry [ctb] (Ionicons), Drifty [cph] (Ionicons), Aidan Lister [ctb, cph] (jQuery StickyTabs)	http://rmarkdown.rstudio.com	GPL-3	1.8
knitr	Yihui Xie [aut, cre], Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Ben Baumer [ctb], Brian Diggs [ctb], Cassio Pereira [ctb], David Robinson [ctb], Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty), Doug Hemken [ctb], Duncan Murdoch [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. Smith [ctb], Kirill Mueller [ctb], Kohske Takahashi [ctb], Michael Friendly [ctb], Michal Bojanowski [ctb], Michel Kuhlmann [ctb], Nacho Caballero [ctb], Nick Salkowski [ctb], Noam Ross [ctb], Qiang Li [ctb], Ramnath Vaidyanathan [ctb], Richard Cotton [ctb], Robert Krzyzanowski [ctb], Romain Francois [ctb], Scott Kostyshak [ctb], Sebastian Meyer [ctb], Sietse Brouwer [ctb], Simon de Bernard [ctb], Sylvain Rousseau [ctb], Taiyun Wei [ctb], Thibaut Assus [ctb], Thibaut Lamadon [ctb], Thomas Leeper [ctb], Tom Torsney-Weir [ctb], Trevor Davis [ctb], Viktoras Veitas [ctb], Weicheng Zhu [ctb], Wush Wu [ctb], Zachary Foster [ctb]	https://yihui.name/knitr/	GPL	1.17
svglite	Hadley Wickham [aut], Lionel Henry [aut, cre], T Jake Luciani [aut], Matthieu Decorde [aut], Vaudor Lise [aut], Tony Plate [ctb] (Early line dashing code), David Gohel [ctb] (Line dashing code and raster code), Yixuan Qiu [ctb] (Improved styles; polypath implementation), Håkon Malmedal [ctb] (Opacity code), RStudio [cph]	https://github.com/r-lib/svglite	GPL (>= 2)	1.2.1
scales	Hadley Wickham [aut, cre], RStudio [cph]	https://github.com/hadley/scales	MIT + file LICENSE	0.5.0
fastcluster	Daniel Müllner [aut, cph, cre]	http://danifold.net/fastcluster.html	FreeBSD ; GPL-2 ; file LICENSE	1.1.24
gplots	Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, Bill Venables		GPL-2	3.0.1
ctc	Antoine Lucas [email protected], Laurent Gautier [email protected]	http://antoinelucas.free.fr/ctc	GPL-2	1.52.0
amap	Antoine Lucas	http://mulcyber.toulouse.inra.fr/projects/amap/	GPL	0.8-14
dendextend	Tal Galili [aut, cre, cph] (https://www.r-statistics.com), Gavin Simpson [ctb], Gregory Jefferis [aut, ctb] (imported code from his dendroextras package), Marco Gallotta [ctb] (a.k.a: marcog), Johan Renaudie [ctb] (https://github.com/plannapus), The R Core Team [ctb] (Thanks for the Infastructure, and code in the examples), Kurt Hornik [ctb], Uwe Ligges [ctb], Andrej-Nikolai Spiess [ctb], Steve Horvath [ctb], Peter Langfelder [ctb], skullkey [ctb], Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram), Andrie de Vries [ctb] (ggdendro author), Zuguang Gu [ctb] (circlize author), Cath [ctb] (https://github.com/CathG), John Ma [ctb] (https://github.com/JohnMCMa), Yoav Benjamini [ths]	https://github.com/talgalili/dendextend/, https://cran.r-project.org/package=dendextend, https://www.r-statistics.com/tag/dendextend/, https://academic.oup.com/bioinformatics/article/31/22/3718/240978/dendextend-an-R-package-for-visualizing-adjusting	GPL-2 ; GPL-3	1.6.0
VennDiagram	Hanbo Chen		GPL-2	1.6.18
futile.logger	Brian Lee Yung Rowe		LGPL-3	1.4.3
plot3D	Karline Soetaert [email protected]		GPL (>= 3.0)	1.1.1
scatterplot3d	Uwe Ligges [email protected], Martin Maechler, Sarah Schnackenberg		GPL-2	0.3-40
ggplot2	Hadley Wickham [aut, cre], Winston Chang [aut], RStudio [cph]	http://ggplot2.tidyverse.org, https://github.com/tidyverse/ggplot2	GPL-2 ; file LICENSE	2.2.1
RColorBrewer	Erich Neuwirth [aut, cre]		Apache License 2.0	1.1-2
openxlsx	Alexander Walker [aut, cre], Luca Braglia [ctb]	https://github.com/awalker89/openxlsx	GPL-3	4.0.17
GO.db	Marc Carlson		Artistic-2.0	3.5.0
GenomicFeatures	M. Carlson, H. Pagès, P. Aboyoun, S. Falcon, M. Morgan, D. Sarkar, M. Lawrence		Artistic-2.0	1.30.0
AnnotationDbi	Hervé Pagès, Marc Carlson, Seth Falcon, Nianhua Li		Artistic-2.0	1.40.0
AnnotationHub	Martin Morgan [cre], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb]		Artistic-2.0	2.10.1
biomaRt	Steffen Durinck [aut], Wolfgang Huber [aut], Sean Davis [ctb], Francois Pepin [ctb], Vince S Buffalo [ctb], Mike Smith [ctb, cre]		Artistic-2.0	2.34.1
rtracklayer	Michael Lawrence, Vince Carey, Robert Gentleman		Artistic-2.0 + file LICENSE	1.38.2
Cairo	Simon Urbanek [email protected], Jeffrey Horner [email protected]	http://www.rforge.net/Cairo/	GPL-2	1.5-9
reshape2	Hadley Wickham [email protected]	https://github.com/hadley/reshape	MIT + file LICENSE	1.4.3
R6	Winston Chang [aut, cre]	https://github.com/wch/R6/	MIT + file LICENSE	2.2.2
DESeq2	Michael Love, Simon Anders, Wolfgang Huber	https://github.com/mikelove/DESeq2	LGPL (>= 3)	1.18.1
SummarizedExperiment	Martin Morgan, Valerie Obenchain, Jim Hester, Hervé Pagès		Artistic-2.0	1.8.1
DelayedArray	Hervé Pagès		Artistic-2.0	0.4.1
matrixStats	Henrik Bengtsson [aut, cre, cph], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Dongcan Jiang [ctb], Peter Langfelder [ctb]	https://github.com/HenrikBengtsson/matrixStats	Artistic-2.0	0.52.2
Biobase	R. Gentleman, V. Carey, M. Morgan, S. Falcon		Artistic-2.0	2.38.0
GenomicRanges	P. Aboyoun, H. Pagès, and M. Lawrence		Artistic-2.0	1.30.0
GenomeInfoDb	Sonali Arora, Martin Morgan, Marc Carlson, H. Pagès		Artistic-2.0	1.14.0
IRanges	H. Pagès, P. Aboyoun and M. Lawrence		Artistic-2.0	2.12.0
S4Vectors	H. Pagès, M. Lawrence and P. Aboyoun		Artistic-2.0	0.16.0
BiocGenerics	The Bioconductor Dev Team		Artistic-2.0	0.24.0
colourpicker	Dean Attali [aut, cre], David Griswold [ctb]	https://github.com/daattali/colourpicker	MIT + file LICENSE	1.0
shinyjs	Dean Attali [aut, cre]	http://deanattali.com/shinyjs	AGPL-3	0.9.1
shinyBS	Eric Bailey	https://ebailey78.github.io/shinyBS	GPL-3	0.61
DT	Yihui Xie [aut, cre], Joe Cheng [ctb], JJ Allaire [ctb], jQuery contributors [ctb, cph] (jQuery in htmlwidgets/lib), SpryMedia Limited [ctb, cph] (DataTables in htmlwidgets/lib), Brian Reavis [ctb, cph] (selectize.js in htmlwidgets/lib), Leon Gersen [ctb, cph] (noUiSlider in htmlwidgets/lib), Bartek Szopka [ctb, cph] (jquery.highlight.js in htmlwidgets/lib), RStudio Inc [cph]	http://rstudio.github.io/DT	GPL-3 ; file LICENSE	0.2
htmltools	RStudio, Inc.	https://github.com/rstudio/htmltools	GPL (>= 2)	0.3.6
markdown	JJ Allaire [aut], Jeffrey Horner [aut], Henrik Bengtsson [ctb], Jim Hester [ctb], Yixuan Qiu [ctb], Kohske Takahashi [ctb], Adam November [ctb], Nacho Caballero [ctb], Jeroen Ooms [ctb], Thomas Leeper [ctb], Joe Cheng [ctb], Andrzej Oles [ctb], Vicent Marti [aut, cph] (The Sundown library), Natacha Porte [aut, cph] (The Sundown library), RStudio [cph], Yihui Xie [cre, ctb]	https://github.com/rstudio/markdown	GPL-2	0.8
shiny	Winston Chang [aut, cre], Joe Cheng [aut], JJ Allaire [aut], Yihui Xie [aut], Jonathan McPherson [aut], RStudio [cph], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/www/shared/jqueryui/AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Stefan Petre [ctb, cph] (Bootstrap-datepicker library), Andrew Rowls [ctb, cph] (Bootstrap-datepicker library), Dave Gandy [ctb, cph] (Font-Awesome font), Brian Reavis [ctb, cph] (selectize.js library), Kristopher Michael Kowal [ctb, cph] (es5-shim library), es5-shim contributors [ctb, cph] (es5-shim library), Denis Ineshin [ctb, cph] (ion.rangeSlider library), Sami Samhuri [ctb, cph] (Javascript strftime library), SpryMedia Limited [ctb, cph] (DataTables library), John Fraser [ctb, cph] (showdown.js library), John Gruber [ctb, cph] (showdown.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), R Core Team [ctb, cph] (tar implementation from R)	http://shiny.rstudio.com	GPL-3 ; file LICENSE	1.0.5

Required packages

Updating this README file

This README file is autogenerated using RMarkdown. Please don’t forget to run PCAGO once before rebuilding this README.

Note: You cannot use RStudio as RStudio’s RMarkdown builder runs in a separate environment!

# Run PCAGO once
shiny::runApp()
# Cancel with Ctrl + C
# Build the README file
rmarkdown::render("README.Rmd")

Credits

Uses code from https://github.com/daattali/advanced-shiny by Dean Attali. Licensed under the MIT license.