CAGEd-oPOSSUM Download

You may download and install your own local copy of CAGEd-oPOSSUM.
Please see the INSTALL file included in the top-level of the CAGEd-oPOSSUM source code for details on how to perform a local installation.

Web Download

Download the full CAGEd-oPOSSUM source code including the API, stand-alone analysis scripts and web code directly from the web page here: CAGEd_oPOSSUM.tar.gz

GitHub

The CAGEd-oPOSSUM source code is also available as a public repository on GitHub at: https://github.com/wassermanlab/CAGEd-oPOSSUM.

Databases

There are two CAGEd-oPOSSUM databases of pre-computed transcription factor binding sites, one for each species:

CAGEd_oPOSSUM_human
CAGEd_oPOSSUM_mouse

As well there is our local copy of the JASPAR database of transcription factor binding site profiles:

JASPAR_2016

By far the preferred way to download these databases is via our FTP site as CAGEd-oPOSSUM human and mouse databases are quite large (tens of Gigabytes).

The two CAGEd-oPOSSUM species database are located in the CAGEd_oPOSSUM/databases sub-directory and the JASPAR database is located in the JASPAR_2016 sub-directory.

As the JASPAR database is quite small you may also download it directly from the database server using the mysldump facility.
NOTE: It is necessary to use the --skip-lock-tables option when using mysqldump.

The JASPAR_2016 database is hosted on our vm5.cmmt.ubc.ca server and may be downloaded using the MySQL user jaspar_r:

    $ mysqldump -h vm5.cmmt.ubc.ca -u jaspar_r --skip-lock-tables JASPAR_2016 > JASPAR_2016.sql

As the CAGEd-oPOSSUM human and mouse databases are quite large please download them from our FTP server. If for some reason you are unable to download them via FTP please email us a 'opossum AT cmmt DOT ubc DOT ca' and we will try to rectify the problem or grant you permission to directly mysqldump them from our servers.