RDATKit (RNA Dataset ToolKIT)

RDATkit is a set of tools for parsing, analyzing, and publishing data of RNA chemical footprinting assays. It allows researchers to share their data using community standard formats, and helps them publish their results on indexable and shareable databases.

RDATKit is a package provides a set of Python and MATLAB scripts that facilitate saving and loading data to and from files with RDAT format. It also supports the ISATAB file format.

Installation

MATLAB

Download the zip or tar file of the repository and unpack; or

git clone https://github.com/ribokit/RDATKit.git

In MATLAB, go to "Set Path". Then "Add with Subfolders" of the target path/to/RDATKit/MATLAB/.

Python

To install RDATKit, simply:

Copy path.py.example into rdatkit/path.py. Edit rdatkit/path.py following the instructions in the file to point to local installations of RNAstructure, ViennaRNA, and VARNA.
Run:

cd path/to/RDATKit/
python setup.py install

For system-wide installation, you must have permissions and use with sudo.

RDATKit requires the following Python packages as dependencies, all of which can be installed through pip.

numpy >= 1.8.0
scipy >= 0.13.0
xlrd >= 0.9.2
xlwt >= 1.0.0

Documentation

Documentation is available at https://ribokit.github.io/RDATKit/.

License

Developed by Das lab, Leland Stanford Junior University.