Consensus Pathway Analysis
Plot pathways heatmap plot from pathway/geneset/meta analysis results
Plot a pathway network
Process and normalize agilent-based dataset
Perform Consensus Analysis
Differential expression analysis
Combine DE analysis results
Get supported platforms
Load data from GitHub
Plot a bar chart of the pathway analysis results
Plot gene heatmap from a SummarizedExperiment object with DE analysis ...
Plot pathway forest plot from pathway/geneset/meta analysis results
Plot KEGG map with DE genes
Plot MA plot from DE analysis results
Get gene sets
Download GEO data
Get KEGG pathway catalogue (network) for CePa.ORA and CePa.GSA methods
Get common significant DE genes from multiple DE Analysis results
Retrieve common significant pathways from multiple pathway analysis re...
Get Entrez annotation
Get KEGG pathway network for SPIA method
Plot Venn diagram from multiple DE Analysis results
Plot Venn diagram from multiple pathway analysis results
Plot volcano plot from Pathway analysis results
Plot volcano plot from Pathway analysis results
Process and normalize affymetrix-based dataset
Gene Set Enrichment Analysis
Topology-based Pathway Analysis
Perform Meta Analysis
Provides a set of functions to perform pathway analysis and meta-analysis from multiple gene expression datasets, as well as visualization of the results. This package wraps functionality from the following packages: Ritchie et al. (2015) <doi:10.1093/nar/gkv007>, Love et al. (2014) <doi:10.1186/s13059-014-0550-8>, Robinson et al. (2010) <doi:10.1093/bioinformatics/btp616>, Korotkevich et al. (2016) <arxiv:10.1101/060012>, Efron et al. (2015) <https://CRAN.R-project.org/package=GSA>, and Gu et al. (2012) <https://CRAN.R-project.org/package=CePa>.