RBP group



We developed a computational approach to provide novel insights into combinatorial regulations of RBPs. The downloading of source codes and instructions were provided.
Two programs take a matrix containing non-negative values as an input, each column repersents one CLIP-seq data, each row repersents one binding sites. The optimal rank can be selected according to the results of NMF.estimate.R The basis matrix and coefficient matrix as the main results can be used for further predicting RNA binding protein groups and potential functions for binding sites.

Installation and Usage

We provide source code of our RBPgroup method on github (under the GNU 3.0 lincense) and Zenodo (DOI: 10.5281/zenodo.841020).

1. Type git clone https://github.com/lulab/RBPgroup.git or click the download button to download the current version of RBPgroup scripts.

2. Extract the tar file to the directory by typing 'tar -zxvf RBPgroup_codes.tar.gz'

3. A directory named "RBPgroup_codes" will appear. Switch to it by typing 'cd RBPgroup_codes'

4. Type 'Rscript ./NMF.estimate.R -h' and 'Rscript ./NMF.main.R -h' to learn how to use the program.


There are two core program named NMF.estimate.R and NMF.main.R. To run them, it's like to run any other R program. If you don't specify any options, it will give the help options.

Please check more details on GitHub https://github.com/lulab/RBPgroup