Interactive HTML5 visualization for CRISPR/Cas9 knockout screen experiments.
Project description
VISPR is a visualization framework for CRISPR/Cas9 knockout screen experiments. To install VISPR, we recommend the Miniconda Python distribution (see below). Currently, VISPR is under heavy development and not yet recommended for public use.
Installation
The easiest way to install VISPR is to use the Miniconda Python distribution (http://conda.pydata.org/miniconda.html). We recommend to use the Python 3.4 variant. With miniconda installed, you can issue
conda install -c johanneskoester vispr
to install VISPR with all dependencies. To update vispr, you can issue
conda update -c johanneskoester vispr
Usage
After successful installation, you can run VISPR by executing the command
vispr server path/to/config.yaml
This starts a server process. The VISPR user interface will be rendered in a webbrowser. See below for the config file format. If you only want to test VISPR, you can run a test instance with example data by executing
vispr test
Configuring VISPR
VISPR takes MAGeCK and FastQC results as input. These are provided along with additional parameters as config files. One config file defines one set of results (i.e. one experiment). VISPR can be invoked with multiple config files (i.e. multiple experiments), allowing to select and compare experiments via the user interface. The command
vispr config
prints a config file template to the terminal.
Installing VISPR with another Python distribution (for experts)
Make sure that you have numpy, scipy, scikit-learn and pandas installed. Else, their automatic compilation with the command below would take very long. Then, you can issue
pip install vispr
or
pip install vispr –user
if you want to install VISPR without admin rights. All remaining dependencies will be installed automatically.
License
Licensed under the MIT license (http://opensource.org/licenses/MIT). This project may not be copied, modified, or distributed except according to those terms.
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