Scoring functions for the dream / sage challenges
Project description
- note:
DREAMTools is tested for Python 2.7
- Contributions:
Please join https://github.com/dreamtools/dreamtools and share your notebooks https://github.com/dreamtools/dreamtools/notebooks
- Online documentation:
- Issues and bug reports:
Overview
DREAMTools aims at sharing code used in the scoring of DREAM challenges.
The main goals are to provide:
scoring functions for the Dream challenges for end-users via the dreamtools-scoring standalone application.
a place for developers involved in the dream challenges to share code
DREAMTools does not provide code related to aggregation, leaderboards, or more complex analysis even though such code can be provided (e.g. D8C1 challenge). Note that some functionalities may be restricted with some access to synapse platform. Indeed, some challenges will require to download public data sets from Synapse (in which case you will need to register).
Installation
DREAMTools depends on a few libraries such as Pandas, Numpy, Matplotlib. They should be automatically installed with dreamtools using pip executable:
pip install dreamtools
From source, download the source code and install the package with Python:
git clone git@github.com:dreamtools/dreamtools.git cd dreamtools sudo python setup.py install
The dreamtools-scoring executable
For users, DREAMTools provides an executable called dreamtools, which should be installed automatically. Knowing the name of the challenge (and possibly sub-challenge), it works as follows:
dreamtools --challenge d8c1 --sub-challenge sc1a --submission example.zip
It prints some information and the score of the submision for instance for the example above:
Solution for alphabeta-Network.zip in challenge d8c1 (sub-challenge sc1a) is : AUROC: 0.803628919403 Rank LB: 1
Available challenges
DREAMTools includes about 80% of DREAM challenges from DREAM2 to DREAM9.5
Templates
All template location can be retrieved using dreamtools executable:
dreamtools --challenge d5c2 --download-template
Gold standard
All gold standard are retrieved automatically. You can obtain a GS location as follows:
dreamtools --challenge d5c2 --download-goldstandard
Issues
Please fill bug report in https://github.com/dreamtools/dreamtools/issues
Contributions
Please join https://github.com/dreamtools/dreamtools
For developers
Please see doc/source/developers.rst
Credits
Please see doc/source/credits.rst
Project details
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