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Last Commit
Feb. 23, 2018
Created
Mar. 24, 2017


A data mining suite for DNA microarrays

candis is an open source data mining suite (released under the GNU General Public License v3) for DNA microarrays that consists of a wide collection of tools you require, right from Data Extraction to Model Deployment. candis is built on top of the toolkit - CancerDiscover written by the bioinformaticians at HelikarLab.

WARNING: candis currently is still in dev mode and not production-ready yet. In case if you run across bugs or errors, raise an issue over here.

Table of Contents

Installation

Assuming you've installed dependencies, simply

$ pip install candis

TL;DR

$ curl -sL git.io/install-candis | python # with dependencies

... and lauch candis's development server:

$ candis

To install candis right from scratch, check out our exhaustive guides:

Docker Image

You can also attempt to install candis via Docker as follows:

$ docker pull helikarlab/candis

... and simply run the image optionally mapping the port 5000.

$ docker run -p 8888:5000 candis

Usage

Launching the RIA (Rich Internet Application)

via CLI

$ candis

OR

$ python -m candis

via Python

>>> import candis
>>> candis.main()

Using the CLI (Command Line Interface)

$ candis --cdata path/to/data.cdata --config path/to/config.json

Features

  • Converting a CDATA to an ARFF file

     >>> import candis
     >>> cdata = candis.cdata.read('path/to/data.cdata')

    Then, simply use the CData.toARFF API:

     >>> cdata.toARFF('path/to/data.arff')
  • Running a Pipeline.

     >>> pipe = candis.Pipeline()
     >>> pipe.run(cdata)
     >>> while pipe.status == candis.Pipeline.RUNNING:
     ...     # do something while pipeline is running

Dependencies

  • Production Dependencies
    • R
    • WEKA (NOTE: Requires Java)
    • Python 3.6+ and PIP (Python's Package Manager)
    • NumPy
  • Development Dependencies

Team


Dr. Tomas Helikar, Ph.D
[email protected]

Principal Investigator


Dr. Akram Mohammed, Ph.D
[email protected]

Author and Maintainer


Achilles Rasquinha
[email protected]

Author and Maintainer

License

This software has been released under the GNU General Public License v3.