Interactive HTML5 visualization for CRISPR/Cas9 knockout screen experiments.
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VISPR - A visualization framework for CRISPR data.
VISPR is a web-based, interactive visualization framework for CRISPR/Cas9 knockout screen experiments. For recent changes, see the [change log](CHANGELOG.md).
The easiest way to install VISPR is to use the Miniconda3 Python distribution (http://conda.pydata.org/miniconda.html). Make sure you install the Python 3 variant. On Linux or Mac OSX, you can then issue
conda install –channel bioconda vispr
in a terminal to install VISPR with all dependencies using the [Bioconda channel](http://bioconda.github.io).
To update VISPR and all other installed Conda packages, issue
conda update –channel bioconda –all
If you are using an old version of MacOS X and the conda command is not available after installation of Miniconda, you have to change your shell to bash. To do this permanently, issue
chsh -s /bin/bash
All steps below have to be executed in a terminal.
### Step 1: Testing VISPR
After successful installation, you can test VISPR with example data by executing
in a terminal. This will download test data and allow you to explore all features of VISPR.
### Step 2: Configuring VISPR
VISPR takes [MAGeCK](http://liulab.dfci.harvard.edu/Mageck) and [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc) results as input. To display such results in VISPR, you have to provide a config file that points to result files and sets additional parameters. One config file defines one set of results (i.e. one experiment). The easiest way to generate your own data and create vispr config files is to use the [MAGeCK-VISPR](https://bitbucket.org/liulab/mageck-vispr) workflow. If you don’t want to use the workflow, you can manually create a VISPR config by issueing
to obtain a template for modification.
### Step 3: Running VISPR
Once you have a config file (either generated by the workflow or manually), you can issue
vispr server path/to/config.yaml
to start a server process that renders the VISPR user interface in a webbrowser. VISPR can be invoked with multiple config files (i.e. multiple experiments), allowing to select and compare experiments via the user interface.
Further, you can compress results into an archive that can easily be sent via email:
vispr archive path/to/config.yaml myexperiment.tar.bz2
Then, even on a different workstation, the results can be extracted and visualized with VISPR:
tar -xf myexperiment.tar.bz2 vispr server myexperiment/vispr.yaml
For further help, explore all command line options of VISPR with
### Step 4: Running VISPR on remote server
The latest version of VISPR now allows users to visit VISPR server from a remote machine (thanks to Wubing Zhang). Simply add use the “–host <your ip address>” option in server and test command to allow remote visit. For example, if your ip address is 192.168.86.164, you can run
vispr test –host 192.168.86.164 –port 5000
in the server, and remotely access VISPR by typing 192.168.86.164:5000 in another computer’s browser.
Similarly, you can use
vispr server myexperiment/vispr.yaml –host 192.168.86.164 –port 5000
to allow remote access of the content in myexperiment/vispr.yaml
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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