qiyunzhu / ezcalour

GUI for Calour functions

EZCalour

Full GUI for Calour functions

Installation:

1. Install Calour:

Follow instructions Here

2. Install EZCalour:

pip install git+git://github.com/amnona/EZCalour.git

Usage:

To run EZCalour, just type from a command prompt:

source activate calour

ezcalour.py

Keyboard shortcuts for the heatmap are described 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 using "Filter" in the "Samples" tab

3. Cluster features (so similar behaving features will be close to each other) using "Cluster" in the "Features" tab

4. Plot