معرفی شرکت ها
dreamtools-1.3.0
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشترتوضیحات
Scoring functions for the DREAM / SAGE challenges
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | dreamtools-1.3.0 |
| نام | dreamtools |
| نسخه کتابخانه | 1.3.0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Thomas Cokelaer |
| ایمیل نویسنده | cokelaer@gmail.com |
| آدرس صفحه اصلی | https://github.com/dreamtools/dreamtools |
| آدرس اینترنتی | https://pypi.org/project/dreamtools/ |
| مجوز | BSD |
############################################################################
DREAMTools
############################################################################
.. image:: https://badge.fury.io/py/dreamtools.svg
:target: https://pypi.python.org/pypi/dreamtools
.. image:: https://secure.travis-ci.org/dreamtools/dreamtools.png
:target: http://travis-ci.org/dreamtools/dreamtools
.. image:: https://coveralls.io/repos/dreamtools/dreamtools/badge.png?branch=master
:target: https://coveralls.io/r/dreamtools/dreamtools?branch=master
.. image:: https://zenodo.org/badge/18543/dreamtools/dreamtools.svg
:target: https://zenodo.org/badge/latestdoi/18543/dreamtools/dreamtools
.. image:: http://readthedocs.org/projects/dreamtools/badge/?version=latest
:target: http://dreamtools.readthedocs.org/en/latest/?badge=latest
:alt: Documentation Status
:Python version: DREAMTools is supported for Python 2.7, 3.4 and 3.5.
Pre-compiled versions are available for Linux and MAC platforms through Anaconda
and the **bioconda** channel.
:Note about coverage: We do not run the entire test suite on Travis, which
reports a 40% test coverage. Note however, that the actual
test coverage is about 80%.
:Contributions: Please join https://github.com/dreamtools/dreamtools
:Online documentation: `On readthedocs <http://dreamtools.readthedocs.org/>`_
:Issues and bug reports: `On github <https://github.com/dreamtools/dreamtools/issues>`_
:How to cite: Cokelaer T, Bansal M, Bare C et al. DREAMTools: a Python
package for scoring collaborative challenges [version 1; referees:
awaiting peer review] F1000Research 2015, 4:1030
(doi: 10.12688/f1000research.7118.1)
`F1000 link <http://f1000research.com/articles/4-1030/v1>`_
.. won't appear on github but within the sphinx doc
.. image:: ../dreamtools_logo.png
:width: 50%
.. contents::
Overview
----------------
Motivation
~~~~~~~~~~~~
**DREAMTools** aims at sharing code used in the scoring of `DREAM <http://dreamchallenges.org>`_ challenges that pose fundamental questions about system biology and translational medicine.
The main goals of **DREAMTools** are to provide:
#. Scoring functions equivalent to those used during past DREAM challenges for **end-users** via a standalone application (called **dreamtools**).
#. A common 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
may be provided (e.g., in D8C1 challenge).
Note that many scoring functions requires data hosted on `Synapse <http://www.synapse.org>`_ . We therefore strongly encourage you to **register to Synapse**. Depending on the challenge, you may be requested to accept terms of agreements to use the data.
Installation
-----------------
For those familiar with Python, you may use the `pip executable <https://pypi.python.org/pypi/pip>`_ provided with Python. It will install the latest release of **DREAMTools** and the dependencies::
pip install cython
pip install dreamtools
If you are not familiar with compilation and/or Python, you may use `conda <https://www.continuum.io/downloads>`_ since we have pre-compiled packages with a conda channel called **bioconda**::
conda config --add channels r
conda config --add channels bioconda
conda install dreamtools
See `Installation section on RTD <http://dreamtools.readthedocs.org/en/latest/installation.html#installation>`_ for details.
Usage
~~~~~~~~~
**DREAMTools** can be used by developers as a Python package::
>>> from dreamtools import D6C3
>>> s = D6C3()
>>> s.score(s.download_template())
{'results': chi2 53.980741
R-square 34.733565
Spearman(Sp) 0.646917
Pearson(Cp) 0.647516
dtype: float64}
A standalone application can be used from a terminal. The executable is called **dreamtools**. Here is an example::
dreamtools --challenge D6C3 --submission path_to_a_file
See `online documentation on <dreamtools.rtd.org for details>`_ for more details
and examples. The source code also provides a set of IPython/Jupyter notebooks.
Available challenges, templates and gold standards
--------------------------------------------------------
**DREAMTools** includes about 80% of DREAM challenges from DREAM2 to DREAM9.5
Please visit `F1000 link <http://f1000research.com/articles/4-1030/v1>`_ (Table 1).
All gold standards and templates are retrieved automatically. Once downloaded, you
can obtain the location of a gold standard or template as follows::
dreamtools --challenge D6C3 --download-gold-standard
dreamtools --challenge D6C3 --download-template
See `online documentation on RTD <http://dreamtools.readthedocs.org/>`_ for details.
نحوه نصب
نصب پکیج whl dreamtools-1.3.0:
pip install dreamtools-1.3.0.whl
نصب پکیج tar.gz dreamtools-1.3.0:
pip install dreamtools-1.3.0.tar.gz