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.
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
- Use our Docker Image (recommended)
Big thanks go out to Lasse Faber!
docker run -p 8000:8000 --user $(id -u):$(id -g) --rm -it mhoelzer/pcago:1.0--c1e506c ./run_packrat.sh
Run the docker container in the same way like above and additionally connect to the server with port forwarding.
ssh -L 8000:127.0.0.1:8000 your@your.server.com
In both cases you will then be able to access the PCAGO-Server via the following address in your browser: 127.0.0.1:8000.
Download the PCAGO-Electron here. This application wraps a PCAGO-server within an Electron application.
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()
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.
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:
- Download the package sources
- Unpack them into the
packratdirectory within the PCAGO project folder - Start R within the project directory
- 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.
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")
| 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 antoinelucas@gmail.com, Laurent Gautier laurent@cbs.dtu.dk | 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 karline.soetaert@nioz.nl | GPL (>= 3.0) | 1.1.1 | |
| scatterplot3d | Uwe Ligges ligges@statistik.tu-dortmund.de, 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 Simon.Urbanek@r-project.org, Jeffrey Horner jeff.horner@vanderbilt.edu | http://www.rforge.net/Cairo/ | GPL-2 | 1.5-9 |
| reshape2 | Hadley Wickham h.wickham@gmail.com | 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
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")
Uses code from https://github.com/daattali/advanced-shiny by Dean Attali. Licensed under the MIT license.