ANANSE: ANalysis Algorithm for Networks Specified by Enhancers

What is ANANSE?

ANANSE is a computational approach to infer enhancer-based gene regulatory networks (GRNs) and to identify key transcription factors between two GRNs. You can use it to study transcription regulation during development and differentiation, or to generate a shortlist of transcription factors for trans-differentiation experiments.

ANANSE is written in Python and comes with a command-line interface that includes the following commands:

Command	Function
ananse binding	predict transcription factor binding profiles
ananse network	infer a gene regulatory network
ananse influence	infer key transcription factors between two networks
ananse plot	plot influence results in a dotplot and optionally a GRN of the Top TFs
ananse view	inspect the output of ananse binding

All functionality is also available through a Python API.

ANANSE is free and open source research software. If you find it useful please cite it:

ANANSE can also be useful when using CAGE-seq data. If you used this tool with CAGE-seq data, please cite:

Getting started

• Install ANANSE on Linux or Mac, see the Installation page for details.
• Have a look at these simple examples to get a taste of what is possible.
• Check out the command-line reference to get going with your own data.

Get help

• First, check the FAQ for common issues.
• The preferred way to get support is through the Github issues page.
• Finally, you can reach us by email to Simon J. van Heeringen or Quan Xu.

Full contents

• Model description
  • Overview of ANANSE
  • Prediction of transcription factor binding
  • Inference of gene regulatory networks
  • Calculation of influence score
• Installation
  • The easiest way to install
  • Alternative installation
• Input data
  • Genome
  • Motif database
  • Enhancer regions
  • Enhancer activity
  • Expression data
  • Differential expression data
  • CAGE-seq
• Command-line reference
  • Command: ananse binding
  • Command: ananse network
  • Command: ananse influence
  • Command: ananse plot
  • Command: ananse view
• API documentation
  • Working with the binding Class
  • Working with the network Class
  • Working with the influence Class
• Examples
  • Ananse setup
  • Example of ananse binding
  • Example of ananse network
  • Example of ananse influence
• FAQ
  • I can apply ANANSE to what kind of enhancer data
  • I can apply ANANSE to what bioogy process
  • I can apply ANANSE to which species data
  • Do I need provide motif data
• Acknowledgments