Table of Contents

There are currently no required Pythom modules for the core Cell Browser script: cbBuild. Installation instructions for a variety of methods are below, with pip being the recommended method.

Basic installation

With conda

If you would prefer to install the Cell Browser through bioconda, you can run:

conda install -c bioconda ucsc-cell-browser

There should be conda versions for release 0.4.23 onwards. Please indicate in any bug reports if you used conda to install.

With git clone

Pip is not required to install the Cell Browser. As an alternative to pip or conda, you can also git clone the repo and run the command line scripts under cellbrowser/src:

git clone --depth=10
cd cellBrowser/src

With wget or curl

You don’t use pip, conda or git? You can also download the current master branch:


Notes on Windows Installation

First install the Windows Linux subsystem. Then open the Windows Linux Subsystem bash terminal and run these commands:

sudo apt-get update
sudo apt-get install python-pip
sudo pip install cellbrowser

Optional modules

To take advantage of some of the advanced features or specialized scripts such as cbScanpy or cbSeurat, you will need to install some extra packages or tools.

Image sizes

To get the image sizes, cbBuild uses either the “file” command or the “identify” command (for JPEGs). You may have to install the ImageMagick package to get the identify command.

Custom Colors

In your cellbrowser.conf you can specify a file with custom colors for your metadata values. If this file contains HTML color names instead of color codes, you have to install the module webcolors:

pip install webcolors

Matrices in mtx format

To read expression matrices in .mtx format, you have to install scipy:

pip install scipy

cbScanpy and cbSeurat

cbScanpy requires that Scanpy is installed.

cbSeurat requires that both R and Seurat are installed .