List of databases for the cisTarget family of tools (e.g. RcisTarget, SCENIC/pySCENIC, and cisTopic).

To choose the database appropiate for your analysis, start by selecting the species and ranking type (i.e. What do you want to analyze: genes or regions?).

Note that the download size is typically over 1GB (100GB for mammal region databases), we recommend downloading the files with zsync_curl (see the Help with downloads).

Related files:

Column info:


Ranking type:

Distance: For gene rankings only. Indicates the search space around the TSS of gene in which the motif is scored:

Motif or track collection:

nOrt: Number of orthologous species used to select the regions based on conservation. In case of doubt of which version to use: 7 species is normally appropiate for most analyses.

Genome: Genome version used to construct the ranking. For region-based analyses it is important that this version matches your data! Gene annotation version is shown in parenthesis.

Database name: Database name (add the extensions to obtain specific file names, e.g. .feather or .feather.zsync).

Download URL: Link to the database (.feather file, and its size).

List of databases:

Last updated: 03 Feb 2021, 14:51