correlationplus

A Python package to calculate, visualize and analyze correlation maps of proteins.

correlationplus contains four main scripts that you can use to calculate, visualize and analyze correlation maps of proteins. These correlations can be dynamical cross-correlations, linear mutual information, sequence based covariation/coevolution or any other pairwise coupling metric. You can use elastic network models or your molecular dynamics trajectories for calculation of dynamical correlations.

Video Tutorials

• Installation: https://www.youtube.com/watch?v=Fc_xpnrbbWU
• Calculate Module: https://www.youtube.com/watch?v=HG8Mzmy1IOM
• Visualize Module: https://www.youtube.com/watch?v=HgUVAV1unXs
• Analyze Module: https://www.youtube.com/watch?v=04BwJDauOn4
• Sequence Conservation Analysis with CoeViz and correlationplus (Part 1): https://www.youtube.com/watch?v=ieu91glEd0s
• Sequence Conservation Analysis with CoeViz and correlationplus (Part 2): https://www.youtube.com/watch?v=BuxQNFoid1A

Installation

We recommend one of the installation methods for regular users:

with conda

conda install -c bioconda correlationplus

with pip

The pip version required by some dependencies is >= 21.0.1, which is not the pip version bundle with python 3.(6,7,8) So, you have to update pip before installing correlationplus. Otherwise, you will have trouble during MDAnalysis dependency installation. For this reason, we strongly encourage you to install correlationplus in a virtualenv.

python3 -m venv correlationplus
cd correlationplus
source bin/activate
python3 -m pip install -U pip
python3 -m pip install correlationplus

if you still want to install it without using a virtualenv or you hate to upgrade pip version to a version >=21.0.1, install numpy==1.16 and the install correlationplus

We recommend to use pip as follows:

python3 -m pip install numpy==1.16.1
python3 -m pip install correlationplus

or if you do not have administration rights

python3 -m pip install --user numpy==1.16.1
python3 -m pip install --user correlationplus

Most of the time, at least one these methods will be sufficient for the installation. However, if these two methods didn't work for any reason, you can take a look to 'Advanced Installation' instructions at https://correlationplus.readthedocs.io/en/latest/installation.html#advanced-installation.

Quickstart

There are four main scrips:

• calculate
• visualize
• analyze
• paths

You can find details of each script with the following commands:

correlationplus calculate -h
correlationplus visualize -h
correlationplus analyze -h
correlationplus paths -h

Go to our readthedocs for detailed usage examples for each script.

Licensing

correlationplus is developed and released under GNU Lesser GPL Licence. Please read to the COPYING and COPYING.LESSER files to know more.