Package: vispr
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[![Anaconda-Server Badge](https://anaconda.org/bioconda/vispr/badges/downloads.svg)](https://anaconda.org/bioconda/vispr)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).InstallationThe easiest way to install VISPR is to use theMiniconda3Python distribution (http://conda.pydata.org/miniconda.html). Make sure you install the Python 3 variant.
On Linux or Mac OSX, you can then issueconda install –channel bioconda visprin aterminalto install VISPR with all dependencies using the [Bioconda channel](http://bioconda.github.io).To update VISPR and all other installed Conda packages, issueconda update –channel bioconda –allIf you are using an old version of MacOS X and thecondacommand is not available after installation of Miniconda, you have to change your shell tobash. To do this permanently, issuechsh -s /bin/bashUsageAll steps below have to be executed in aterminal.### Step 1: Testing VISPRAfter successful installation, you can test VISPR with example data by executingvispr testin a terminal. This will download test data and allow you to explore all features of VISPR.### Step 2: Configuring VISPRVISPR 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 issueingvispr configto obtain a template for modification.### Step 3: Running VISPROnce you have a config file (either generated by the workflow or manually), you can issuevispr server path/to/config.yamlto 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.bz2Then, even on a different workstation, the results can be extracted and visualized with VISPR:tar -xf myexperiment.tar.bz2
vispr server myexperiment/vispr.yamlFor further help, explore all command line options of VISPR withvispr –help### Step 4: Running VISPR on remote serverThe 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 runvispr test –host 192.168.86.164 –port 5000in the server, and remotely access VISPR by typing 192.168.86.164:5000 in another computer’s browser.Similarly, you can usevispr server myexperiment/vispr.yaml –host 192.168.86.164 –port 5000to allow remote access of the content in myexperiment/vispr.yamlAuthorJohannes Köster <koester@jimmy.harvard.edu>
Wei Li <li.david.wei@gmail.com>LicenseLicensed under the MIT license (http://opensource.org/licenses/MIT). This project may not be copied, modified, or distributed except according to those terms.