R-chie [ɑrči]
A web server and R package for plotting RNA secondary structures, trans RNA-RNA interactions and genomic interactions.
× News!New R4RNA package will be available for download after publishing the manuscript.

R4RNA R Package

R-chie is powered by the R4RNA package, freely available for use under the GNU General Public License (v3). This webpage currently refers to the published version of R4RNA, we will update it with a new source code as soon as the manuscript has been accepted for publication.

(old) Package source: R4RNA_0.1.4.tar.gz
Git repository: R4RNA and R-chie
Reference manual: R4RNA-manual.pdf
(old) Tutorial vignette: R4RNA.pdf
Tutorial vignette 2.0: R4RNA_2.0.pdf
News/ChangeLog:NEWS

R-chie Offline

The offline version of R-chie, which requires first installing R4RNA is available here, or clone our git repository here


How to use:

  1. Ensure R is installed already, or download it freely from http://www.r-project.org/
  2. Download the R4RNA (above) and install the package
  3. Install the optparse and RColorBrewer packaged in the same manner and any other required depencies
  4. Download R-chie, and run it using "Rscript rchie.R --help", or configuring the shebang (first line of script) and executing it directly.

R4RNA Package Features

Check out the tutorial vignette for a short demo of how to use functions in the package. All figures created by the web interface are possible using the package with just a few command calls.

Features:

  • Customized figure legends and titles
  • Customized figure sizes, resolution, and file formats
  • Visualization of very large structures and alignments
  • Customzied width and styles for arcs, lines, and text
  • Convert formats between vienna, connect, bpseq and helix
  • Colour basepairs by frequency from an ensemble of structures
  • Mass produce diagrams with automated scripts
  • ... and more