hCoCena is an R-package that allows you to comprehensively and easily analyse your transcriptomics data. It also provides the option to integrate several datasets using a network-based integration approach and analyse them jointly. Tutorials and a Docker image exist to help you get to know the tool.
hCoCena offers a suite of functionalities that you can pick & mix to create a custom gene co-expression analysis for your transcriptomics data.
If you have more than one dataset that you want to analyse jointly, hCoCena provides you with the option to conduct a network-based integration to merge your datasets prior to the analysis.
The tool comes as an R-package together with an extensive and interactive tutorial as well as a Docker image to make the introduction to the tool as smooth as possible.
While hCoCena offers already a wide variety of analysis options you can choose from, custom function can easily be added.
An extensive Wiki is part of the GitHub repository, providing a lot of background information on functions, underlying methods and the structure of the hCoCena object (hcobject).
More details including a showcase analysis an be found in the paper.