🎀 A data mining suite for gene expression data.
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
.github
R
builder
candis
docs
notebooks
res
.babelrc
.gitignore
.travis.yml
Dockerfile
LICENSE
MANIFEST.in
Makefile
README.md
get-candis
honcho_manager.py
jest.config.js
package.json
package.py
requirements.txt
runtime.txt
setup.cfg
setup.py
webpack.config.js
yarn.lock

README.md


A data mining suite for gene expression data

candis is an open source data mining suite (released under the GNU General Public License v3) for gene expression data 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 helikarlab/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
thelikar2@unl.edu

Principal Investigator


Dr. Akram Mohammed, Ph.D
amohammed3@unl.edu

Author and Maintainer


Achilles Rasquinha
achillesrasquinha@gmail.com

Author and Maintainer


Rupav Jain
rupavwinchester@gmail.com

Author and Maintainer

License

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