R-chie [ɑrči]
A web server and R package for plotting arc diagrams of RNA secondary structures

R4RNA R Package

R-chie is powered by the R4RNA package, freely available for use under the GNU General Public License (v3)

Package source: R4RNA_0.1.4.tar.gz
Git repository: R4RNA and R-chie
Reference manual: R4RNA-manual.pdf
Tutorial vignette: R4RNA.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