References

References

This section lists R, JavaScript and CSS libraries used by SeqPlots, important conceptual contributions to the software, and publication, where figures generated by SeqPlots are featured.

R project and Bioconductor

• R Core Team (2014). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.
• Bioconductor: Open software development for computational biology and bioinformatics R. Gentleman, V. J. Carey, D. M. Bates, B.Bolstad, M.Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, and others 2004, Genome Biology, Vol. 5, R80. URL http://www.bioconductor.org/.
• RStudio and Inc. (2014). shiny: Web Application Framework for R. R package version 0.10.1. http://shiny.rstudio.com/
• Other CRAN packages: digest, DBI,RSQLite, RJSONIO, plotrix, fields, grid, kohonen, ggplot2, Cairo and parallel
• Bioconductor packages: IRanges, BSgenome, Rsamtools, rtracklayer, GenomicRanges and Biostrings

JavaScript and CSS

• jQuery framework - http://jquery.com
• Bootstrap - http://getbootstrap.com
• DataTables, Table plug-in for jQuery - http://www.datatables.net
• jQuery File Upload Plugin - https://github.com/blueimp/jQuery-File-Upload
• jQuery throttle - http://benalman.com/projects/jquery-throttle-debounce-plugin/
• jQuery Cookie Plugin - https://github.com/carhartl/jquery-cookie
• Modernizer JS library - http://modernizr.com
• JavaScript Templates - https://github.com/blueimp/JavaScript-Templates
• JavaScript Color Picker - http://jscolor.com
• md5-js - https://github.com/wbond/md5-js
• Font Awesome - http://fortawesome.github.io/Font-Awesome
• Google Fonts - https://www.google.com/fonts
• jQuery user interface - http://jqueryui.com (documentation)
• jquery.tocify.js: jQuery Table of Contents - https://github.com/gfranko/jquery.tocify.js (documentation)
• Strapdown https://github.com/arturadib/strapdown (documentation)
• Bootswatch themes - http://bootswatch.com (documentation)
• google-code-prettify - https://code.google.com/p/google-code-prettify (documentation)
• marked - https://github.com/chjj/marked (documentation)

Important conceptual contribution to the project

• Liu T, Ortiz J, Taing L, Meyer C, Lee B, Zhang Y, Shin H, Wong S, Ma J, Lei Y, et al. 2011. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biology 12: R83.
• Thomas Williams, Colin Kelley and others (2010). Gnuplot 4.4: an interactive plotting program. URL http://www.R-project.org/.
• Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M. and Haussler, a. D. (2002). The Human Genome Browser at UCSC. Genome Research. 12:996–1006.
• Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. (2010). BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 1;26(17):2204-7
• Nicol, J.W., Helt, G.A., Blanchard, S.G., Raja, A. and Loraine, A.E. (2009). The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics (Oxford, England). 25:2730–1.
• Thorvaldsdóttir, H., Robinson, J.T. and Mesirov, J.P. (2012). Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in bioinformatics. bbs017

Server deployment

• Shiny Server - https://github.com/rstudio/shiny-server
• ShinyApps - https://github.com/rstudio/shinyapps

Publications containing figures made by SeqPlots

• Chen RA, Stempor P, Down TA, Zeiser E, Feuer SK, Ahringer J. Extreme HOT regions are CpG-dense promoters in C. elegans and humans. Genome Res 24(7):1138-1146 Jul 2014
• Latorre I, Chesney MA, Garrigues JM, Stempor P et al. The DREAM complex promotes gene body H2A.Z for target repression. Genes Dev 2015 Mar 1;29(5):495-500.