PathwayMatcher is a standalone command line tool to match human biomedical data to pathways. Its advanced mapping functions allow matching multiple types of omics data to the Reactome database: lists of genetic variants, gene or protein identifiers, lists of peptides including post-translational modifications, and proteoforms. For example, if a protein is provided with a phosphorylation at a given site, it is possible to match only those pathways involving the protein in the given phosphorylation state. PathayMatcher then exports the reactions and pathways matched, standard overrepresentation analysis, and biological networks.
See our Wiki for more information.
As part of our efforts toward delivering open and inclusive science, we follow the Contributor Convenant Code of Conduct for Open Source Projects.
Despite our efforts at enforcing good practices in our work, like every software, PathwayMatcher might crash, fail to cover specific use cases, not perform as well as expected. We apologize for any inconvenience and will try to fix things to the best of our capabilities. We welcome bug reports, suggestions of improvements, and contributions via our issue tracker.
PathwayMatcher is available in Bioconda.
Install with:
conda install -c bioconda pathwaymatcherand update with:
conda update -c bioconda pathwaymatcher
PathwayMatcher is available in the Galaxy Tool Shed under reactome_pathwaymatcher.
PathwayMatcher is ready to use without any previous requirement at the official European Galaxy Instance
- Install java here unless already available on your machine. Note: Java 1.8 is required.
- Download the latest version of the PathwayMatcher executable here.
- Run PathwayMatcher as detailed here.
See our Wiki for more information.
PathwayMatcher can search for reactions and pathways with various input types, and generates mapping files to the database.
See our Wiki for more information.
The input can be:
See our Wiki for more information.
The output of PathwayMatcher is composed of three files, the Reaction and Pathway mapping, the statistical analysis of the relevant pathways, and biological networks constructed based on the input.
See our Wiki for more information.
Networks files constructed using all the entities in PathwayMatcher are available here. protein* and proteoform* files correspond to the networks obtained using protein and proteoform matching, respectively.
PathwayMatcher is described in Hernández Sánchez et al., doi:10.1101/375097, please use this reference to cite the tool and associated network.
The scripts used to generate the figures of the manuscript are available here. We welcome comments and questions on our manuscript, please do not hesitate to contact us via the issue tracker.
PathwayMatcher is a free open-source project, distributed under the permisive Apache License 2.0.