PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP.

Installation

You can install PureCLIP from Bioconda, from the release tarballs and from source.

Bioconda

Using Conda with an activated Bioconda channel is the easiest way to install PureCLIP:

$ conda install pureclip

Release Tarballs

Alternatively, you can get the source code and binaries for macOS and Linux here.

Galaxy: use PureCLIP online

PureCLIP has also been integrated into the European Galaxy server https://usegalaxy.eu/, an open, web-based platform for accessible, reproducible, and transparent computational biological research and is available here (currently not using latest PureCLIP version).

Thanks to the Freiburg Galaxy Team!

Build from source

Clone the repository

$ git clone https://github.com/skrakau/PureCLIP.git
$ cd PureCLIP

Create a build directory, configure the build and compile

$ mkdir build
$ cd build
$ cmake ../src
$ make

Requirements

• C++14 compliant compiler
• GSL
• cmake 3.0 or newer

Documentation

Please have a look at PureCLIPs documentation.

Citation

Krakau S, Richard H, Marsico A: PureCLIP: Capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data. Genome Biology 2017; 18:240; https://doi.org/10.1186/s13059-017-1364-2