Scoring functions for the DREAM / SAGE challenges
Project description
Similarly for For Windows:
Download Anaconda2 (Python2) for windows
Open an Anaconda prompt (from the Start->All program->Anaconda2->Anaconda Prompt
Download conda_install.bat
Execute the script:
sh conda_install.sh python=2
The dreamtools executable
DREAMTools provides functions to obtain the template and gold standard(s) used in a given challenge. Some challenge have restrictions of data access and require the user to accept conditions of use. Such data are stored on http://www.synapse.org. You will need to create a login/password on www.synapse.org website. The first time you run a challenge within DREAMTools, files will be downloaded from Synapse. You may be asked to accept some conditions of use (e.g. D8C1 challenge) directly on the website.
For users, DREAMTools package provides an executable called dreamtools, which should be installed automatically.
To obtain some help, type:
dreamtools --help
You should see a list of challenges: D2C1,D2C3, D2C3,… Those are aliases to DREAM challenges. Information about a challenge can be (in general) obtained from the Synapse page of the challenge using the –onweb option:
dreamtools --challenge D6C3 --onweb
Brief information can also be printed in the terminal as follows:
dreamtools --challenge D6C3 --info
Next, you may want to score one of your submission. We provide access to templates for each challenge. For instance:
dreamtools --challenge D6C3 --download-template
This command prints the location of the template on your system. Copy that file in local/temporary place. Now that you have a copy of the template, you can fill its contents with your own data and score it (let us assume it is called D6C3_template.txt):
dreamtools --challenge D6C3 --submission D6C3_template.txt
This command should print some information and the score of the submission for instance for the example above, we get the following results:
{'results': chi2 53.980741 R-square 34.733565 Spearman(Sp) 0.646917 Pearson(Cp) 0.647516 dtype: float64}
All outputs will contain a json-like output. The synapse page of the challenge should give information about the scoring methodology.
Note that some challenges (like the D8C1 challenge) have sub-challenges. For instance in D8C1, there are 4 sub-challenges names (e.g., SC1A). So, you would need to be more specific and to provide the name of a sub-challenge. For instance:
dreamtools --challenge D8C1 --download-template --sub-challenge SC1A
The sub-challenge names can be obtained using –info option (see here above). Similarly to the simpler case shown above, you can now score that submission as follows:
dreamtools --challenge D8C1 --sub-challenge SC1A \ --submission D8C1_example.zip
Again, you should get an output with the results:
Solution for alphabeta-Network.zip in challenge d8c1 (sub-challenge sc1a) is : meanAUROC: 0.803628919403
Available challenges
DREAMTools includes about 80% of DREAM challenges from DREAM2 to DREAM9.5 Please visit F1000 link (Table 1).
Gold standards
All gold standards are retrieved automatically. You can obtain the location of a gold standard file as follows:
dreamtools --challenge D6C3 --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
More documentation ?
Please see the doc directory, which is processed and posted on pypi website with each release.
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