Prerequisites
Please install the latest version of Cytoscape from:
http://www.cytoscape.org/. Cytoscape
is needed for network visualization and analysis.
Once you have installed Cytoscape 3.X, CoNet can be installed in Cytoscape via the
App manager. If you want to download the full CoNet package, go to
http://systemsbiology.vub.ac.be/conet
Please also install the Cytoscape plugin CytoCluster
via the App manager.
Please register at the MENA web server:
http://ieg2.ou.edu/MENA/login.cgi
We recommend to use the fast version of LSA, which is easier to install than
the original version. Please download fastLSA from
http://hallam.microbiology.ubc.ca/fastLSA/install/index.html.
Follow the instructions given on the fastLSA web packe to install it.
fastLSA requires g++.
SparCC can be downloaded from
https://bitbucket.org/yonatanf/sparcc. SparCC requires python at least of version 2.3 and
numpy.
Optional
Please register at the QIIME database:
http://www.microbio.me/qiime/.
In order to convert biom files into OTU count tables,
you need to install the biom converter (requires python).
For this tutorial, all required input files can be downloaded from the Files section.
If you have R already installed, install
igraph using the Package Installer.
We will use R only for visualization of SparCC results, so if you are not familiar with R,
you can skip the SparCC visualization step.