This GitHub repository contains sample commands and data that will be used during the Reactome presentation on July 17th (and/or 18th), 2020.
Content Service sample queries used during the presentation can be found in the content-service directory. Both the TwelveTumorsNaturePaper127genes.txt data file and Analysis Service sample queries used during the presentation can be found in the analysis-service directory.The 'TwelveTumorsNaturePaper127Genes.txt' was taken from the supplementary information of Kandoth et. al (2013). Directions for installing Docker and getting the Reactome Graph Database instance running can be found in the graph-database directory.
- Reactome FIViz Official guide - This app allows users to run pathway enrichment analysis on a gene list and visualize results in Cytoscape, which can be used to explore functional relationships among genes in hit pathways. It also accesses the Reactome Functional Interaction (FI) network, which is manually curated and covers up to 60% of human proteins.
- ReactomeGSA R Bioconductor package - Run multi-omics Gene set analyses in R and visualize the results in Reactome.
- Reactome2py Python package - Query Reactome's Content and Analysis services using Python.