Metadata-Version: 2.1
Name: ezcalour
Version: 1.12.4
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
Description: # 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)
        
        
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
Provides-Extra: test
Provides-Extra: coverage
Provides-Extra: doc
