Database of posttranscriptional regulatory elements and function
First, install bedtools, we recommend the latest release:
wget https://github.com/arq5x/bedtools2/archive/master.zip -O bedtools.zip
tar -xf bedtools.zip
cd bedtools2-master
makeThen, create a virtual environment and install doRiNA from source:
python3 -m venv dorina-dev
source activate dorina-dev
git clone https://github.com/dieterich-lab/dorina.git
cd dorina
pip install -r requirements.txt -r test_requirements.txt
pip install .For doRiNA development, please use Python version > 3.4.
Dorina requires the files to be setup locally. Let /path/to/datasets/ be the the setup path.
/path/to/datasets/ should contain :
/path/to/datasets/regulators/path/to/datasets/genomes
Both sub-directories have the same structure:
/path/to/datasets/genomes/{organism}/{assembly}//path/to/datasets/regulators/{organism}/{assembly}/
Regulators can be obtained from (here)[http://dorina.mdc-berlin.de/regulators]. Each bed file should be accompanied with metadata file with the same name, but the .json extension:
{ "id": "d_melanogaster", "label": "Fly", "scientific": "Drosophila melanogaster", "weight": 3}The genome directory contains genome annotation separated into several regions for further filtering.
Given the directory structure is correct, the following command should retrieve the miR-1247 regulators of human genome assembly hg19:
dorina run 'hg19' --seta 'hsa-miR-1247|CLASH' -p /path/to/datasets/ > miR-1247.bedTo list the avaiable data sources, use:
dorina genomes -p /path/to/datasets/ | less
dorina regulators -p /path/to/datasets/ | lessPlease see here
- RNA Binding Proteins obtained by cross-linking and immunoprecipitation derived experiments (CLIP)
- miRNA–RNA interactions obtained by clash experiments
- Predicted RNA interactions
Dorina can filter the regulatory datasets by expression
Retrieves single nucleotide variants co-occurring with regulatory elements
dorina is licensed under the GNU General Public Licence (GPL) version 3.
See LICENSE file for details.
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