ezcalour 1.12.4

EZCalour: GUI frontend tool for Calour microbiome analysis software

EZCalour

Welcome to EZCalour, the point and click GUI for the Calour microbiome analysis software.

EZCalour installation

Simple installers (just download and run):

• Windows

• Mac OSX (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

Documentation

Detailed documentation for using EZCalour can be found here

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 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