laylagerami / maven

Elucidate and visualise a compound's mechanism of action by combining structure-based target prediction with gene expression-based causal reasoning, plus pathway enrichment to put results into biological context. GUI-based (minimal coding experience required).

MAVEN (Mechanism of Action Visualisation and ENrichment)

About MAVEN

MAVEN is an R shiny app which enables integrated bioinformatics and chemoinformatics analysis for mechansism of action analysis and visualisation.

The tool is a collaborative work between the Bender Group at University of Cambridge and Saez Lab at Heidelberg University (Rosa Hernansaiz Ballesteros https://github.com/rosherbal).

Documentation can be found at https://laylagerami.github.io/MAVEN/. MAVEN can be installed locally or as a Docker or Singularity container. For a step-by-step tutorial for exploring the mechanism of action of a query compound, you can view our example using the HER2 inhibitor lapatanib.

Implemented approaches and data:

• Target prediction provided by PIDGIN (BenderGroup/PIDGINv4)
• Prior knowledge network from Omnipath DB (https://omnipathdb.org/)
• SMILES widgets provided by ChemDoodle (zachcp/chemdoodle)
• TF enrichment with DoRothEA (saezlab/dorothea)
• Pathway analysis with PROGENy (saezlab/progeny)
• Causal reasoning with CARNIVAL (saezlab/carnival)
• MSigDb gene sets for network pathway enrichment (http://www.gsea-msigdb.org/gsea/msigdb/index.jsp)
• Helper scripts are provided by saezlab/transcriptutorial

Check out https://github.com/saezlab/shinyfunki for a multi-omic functional integration and analysis platform which implements many of the same tools.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.

maven's Issues

MAVEN needs updates

Since initial development, some updating is required

DONE: CARNIVAL to be upgraded to current bioconductor version (v2.6.2)

To do:

• Update install script
• Update server files
• Test performance with latest solver versions (CBC and CPlex)

Would be nice:

• Add new Gurobi solver

DONE: MSigDB signatures to be updated to current version (v2022.1)

To do:

• Fetch new .gmt files
• Update server file
• Test enrichment and hyperlinking functions

Documentation to be updated

To do:

• Update installation instructions
• Update case study