DepRanker: a gene impact score calculator (prioritization method) for RNAi / CRISPR screen results

Developed by Dutt lab

Version v0.2.0

Features

DepRanker works downstream to the shRNA analysis pipelines like edgeR and accomodates information from gene prioritization tools like ROAST and DEMETER. It integrates gene expression, copy number variation data to rank / prioritize genes from pooled screen data.

DepRanker accepts following input files:

• Toptags file from edgeR shRNA analysis
• ROAST output file
• DEMETER gene score file
• Expression file
• Copy number variation file

Availability and Implementation

The open source DepRanker package is implemented in Python and the source code is available from https://github.com/sanket-desai/depranker-git.

Installation

DepRanker package depends on Numpy and SciPy python package may be installed using pip as follows:

pip3 install --user numpy
pip3 install --user scipy

Download the package using the git clone command as follows:

git clone [email protected]:sanket-desai/depranker-git.git .

Moving into the DepRanker GIT repository, the DepRanker program can be directly run as a python script (2.7 / 3.xx compatible).

Usage

usage: depranker.py [-h] [-roast ROAST_RESULT_FILE]
                    [-toptags EDGER_TOPTAGS_FILE] [-exprs EXPRESSION_FILE]
                    [-cnv COPY_NUMBER_VARIATION_FILE] [-out OUTPUT_FILE]
                    [-min_shrna MINGENES]

DepRanker: A gene impact score calculator (prioritization method) for RNAi / CRISPR screen results
Developed by Dutt lab
Version v0.2.0

optional arguments:
  -h, --help            show this help message and exit
  -roast ROAST_RESULT_FILE
                        Roast result file
  -toptags EDGER_TOPTAGS_FILE
                        EdgeR toptags result file
  -exprs EXPRESSION_FILE
                        Gene expression file
  -cnv COPY_NUMBER_VARIATION_FILE
                        Copy number variation file
  -out OUTPUT_FILE      Ouput file
  -min_shrna MINGENES   Minimum number of shRNA representation (integer)

Example dataset

From within the downloaded DepRanker git repository, the main script can be executed on the test dataset provided with the package as follows:

cd depranker-git
python3 depranker/depranker.py -roast datafile/run2/AWScreen2_roast.csv -toptags datafile/run2/AWScreen2_toptags.csv -exprs datafile/run2/geneexp.csv -cnv datafile/run2/copynumber.csv -out datafile/run2/ouput_rank.txt

Similarly the module can be run for the run1 dataset provided in the datafile directory. The output_rank.txt generated by the tool is the result file containing the impact rank score for genes assessed in the pooled ShRNA screen.

License

This project is licensed under the MIT license.