Metadata-Version: 2.1
Name: ezcalour
Version: 1.12.3
Summary: EZCalour: GUI frontend tool for Calour microbiome analysis software
Home-page: http://microbio.me/calour
Author: calour development team
Maintainer: calour development team
License: GPL
Keywords: microbiome heatmap analysis bioinformatics GUI
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: License :: OSI Approved :: BSD License
Classifier: Environment :: Console
Classifier: Topic :: Software Development :: Libraries :: Application Frameworks
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Operating System :: Unix
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Description-Content-Type: text/markdown
Requires-Dist: matplotlib
Requires-Dist: numpy
Requires-Dist: calour
Requires-Dist: dbbact-calour
Provides-Extra: coverage
Requires-Dist: coverage ; extra == 'coverage'
Provides-Extra: doc
Requires-Dist: Sphinx (>=1.4) ; extra == 'doc'
Provides-Extra: test
Requires-Dist: nose ; extra == 'test'
Requires-Dist: pep8 ; extra == 'test'
Requires-Dist: flake8 ; extra == 'test'

# EZCalour
Welcome to EZCalour, the point and click GUI for the [Calour](https://github.com/amnona/Calour) microbiome analysis software.

<div align="center">
        <img width="23%" src="https://github.com/amnona/EZCalour/blob/master/images/main_gui.png" alt="Main GUI" title="Main GUI"</img>
        <img width="39%" src="https://github.com/amnona/EZCalour/blob/master/images/heatmap.png" alt="Interactive heatmap" title="Interactive heatmap"</img>
        <img width="30%" src="https://github.com/amnona/EZCalour/blob/master/images/enriched.png" alt="DBBact enrichment" title="DBBact enrichment"</img>
</div>

## EZCalour installation
Simple installers (just download and run):

* [Windows](https://sourceforge.net/projects/ezcalour/files/ezcalour_installer.exe/download)

* [Mac OSX](https://sourceforge.net/projects/ezcalour/files/EZCalour.dmg/download) (open the .dmg file and drag the EZCalour icon to the applications folder icon)

Alternatively, you can install via console as part of the calour installation using [these instructions](https://github.com/amnona/EZCalour/blob/master/INSTALLATION.md)

## Documentation
Detailed documentation for using EZCalour can be found [here](https://github.com/amnona/EZCalour/blob/master/using-ezcalour.pdf)

## Simple analysis workflow:
### 1. Load the experiment:

**Amplicon experiment**

1a. Load the data using the "Load" button on the top-left corner

1b. Select the biom table file (mandatory), and the mapping file (optional)

1c. Select "amplicon experiment" from the Type combo box

**Metabolomics experiment**

1a. Load the data using the "Load" button on the top-left corner

1b. Select the csv bucket table file (mandatory), and the mapping file (optional)

1c. If each row in the csv bucket table corresponds to a sample, select "Metabolomics - samples are rows" from the Type combo box. Otherwise, select "Metabolomics - samples are columns"

1d. If you have a GNPS data file (see [here](https://github.com/amnona/gnps-calour) for instructions), you can supply this file in the GNPS file field, in order to get GNPS annotations for each metabolite

### 2. Filter the samples of interest
Select "Filter" in the "Samples" tab, select the values you want to keep (or throw away using the "negate" checkbox)

### 3. Cluster features (so similar behaving features will be close to each other)
Select "Cluster" in the "Features" tab. You can also enter a minimal threshold for keeping features (i.e. throw away features with reads sum over all samples < threshold).

### 4. Plot an interactive heatmap
Select the plot button at the bottom.

You can choose a sample field to sort by, as well as bars for the x and y axis

Keyboard shortcuts for the heatmap are described [here](http://biocore.github.io/calour/generated/calour.heatmap.plot.html#calour.heatmap.plot)



