This repository can be cited in publications using the following DOI:
Also consider citing the corresponding publication listed under References.
In DEEP, standardized computational analysis pipelines are documented in form of so-called Process specifications. A Process document lists required input and reference files, specifies the output generated by the pipeline and provides a step-by-step description of the computational analysis. Processes are in XML format and are rendered into a readable form when opened in a standard web browser (assuming an active internet connection). They are lightweight enough to be send via e-mail to collaboration partners.
If you want to document a new analysis type, i.e., a standardized pipeline, or if you just want to document an analysis specific for a DEEP publication, you can download the Process template file and some basic introductory material in this repository:
Each run of a standardized pipeline is supposed to produce an Analysis metadata document at the end
(named like this: DEEP-ID.PROCESS.DATE.amd.tsv). These are simple tab-separated text files listing all input,
output and reference files as well as non-default parameters in form of key-value entries.
Whereas a Process document has to be manually created and describes an analysis pipeline in generic form,
an Analysis metadata file is created automatically. Consequently, these files are not accessible via this repository.
If you are looking for the Analysis metadata files, please refer to the official DEEP data portal hosted by the DEEP Data Collection Center (DCC - DKFZ Heidelberg).
See the corresponding publication in Oxford Database for details:
"A general concept for consistent documentation of computational analyses", Database 2015
The supplemental material is also available in this repository. Please note that this material is just kept for reference, and is considered outdated. Please do not use it to create new Process documents.