3.2 Resources

Databases

Data

  • Known structure: /BioII/lulab_b/shared/projects/RNA_known_structure

  • icSHAPE: /BioII/lulab_b/shared/projects/icSHAPE

  • RNAex (DMS-seq, PARS, icSHAPE): /BioII/lulab_b/shared/projects/RNAex

  • SHAPE-MaP: /BioII/lulab_b/shared/projects/shape-map

  • RNAStralign: /BioII/lulab_b/shared/projects/RNA_stralign

Software

Scripts

Predict SHAPE data

Project directory: /Share2/home/lulab/shibinbin/projects/Deepfold2

Files:

  • Scripts: bin/

  • icSHAPE data preprocessing: Jobs/icSHAPE_*.sh

  • Notes: notes/*.md

  • Processed icSHAPE data: output/icSHAPE_preprocess/

  • icSHAPE reactivities in HDF5 format: data/icSHAPE/

  • Prediction using neural network: bin/predict_reactivity.py

  • Neural network models (keras): models/

  • Workflows using snakemake: workflows/

  • Predict RNA-protein binding: output/motif_ionmf

  • Jupyter notebooks: jupyter/

Motif discovery

Project directory: /Share2/home/lulab/shibinbin/projects/DeepShape

  • Scripts: bin/

  • Notes: notes/

  • Training and test data: output/rfam/, output/jaspar/

Work reports

Tsinghua Cloud (https://cloud.tsinghua.edu.cn):

Summary slide: DeepShape summary 20190622.pptx

Lu Lab / Lu Lab Shared / 1.Project Progress / 14' Shi Binbin / DeepShape