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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, and lists of peptides including posttranslational modifications.
Please note that PathwayMatcher maps the experimental data to pathways in a systematic and unbiased fashion, without filtering, statistics, or biological inference. We recommend that users interpret the results of the matching using the systems biology method that best suits their experiment and biomedical context.
PathwayMatcher is described here, please use this reference to refer to the tool. 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 was presented at the ASHG 2017, the corresponding poster can be found here.