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Interactive HTML5 visualization for CRISPR/Cas9 knockout screen experiments.

Project Description

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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).

Installation

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

Usage

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

vispr test

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

vispr config

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

vispr –help

### 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

Author

Johannes Köster <koester@jimmy.harvard.edu> Wei Li <li.david.wei@gmail.com>

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.

Release History

Release History

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0.4.14

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