thucombio/deepnet-rbp

Guidance to run deep learning for RBP binding site prediction

1. The original CLIP-seq data can be downloaded from http://www.bioinf.uni-freiburg.de/Software/GraphProt/.

2. RNAshapes for predicting RNA 2D structure can be downloaded from http://bibiserv.techfak.uni-bielefeld.de/rnashapes/. You can also use RNAshapes integrated in the GraphProt package (http://www.bioinf.uni-freiburg.de/Software/GraphProt/).

3. Programs and materials to predict RNA 3D structure using JAR3D can be downloaded from http://rna.bgsu.edu/data/jar3d/models/.

4. Programs of the deep learning framework to predict RBP binding sites are provided in the folder deepnet-master/deepnet/examples/multimodal_dbn_RNAbP/.