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Table 1 A summary of XGR characteristics for tasks achieved and runtime required

From: XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits

Functions Tasks achieved Runtimea
Enrichment analysis
 xEnricher A template for enrichment analysis ~40
 xEnricherGenes Gene-based enrichment analysis using a wide variety of ontologiesb ~40
 xEnricherSNPs SNP-based enrichment analysis using Experimental Factor Ontology on GWAS traits ~70
 xEnricherYours Custom-based enrichment analysis using user-defined ontologies ~5
 xEnrichConciser Removing redundant ones from enrichment outputs ~15
 xEnrichBarplot Barplot of enrichment outputs <1
 xEnrichCompare Side-by-side barplots of comparative enrichment outputs <1
 xEnrichDAGplot DAG plot of enrichment outputs <1
 xEnrichDAGplotAdv DAG plot of comparative enrichment outputs <1
Annotation analysis
 xGRviaGeneAnno Annotation analysis using nearby gene annotations by a wide variety of ontologiesb ~60
 xGRviaGenomicAnno Annotation analysis using a wide variety of genomic annotationsc ~30
Similarity analysis
 xSocialiser A template for similarity analysis ~60
 xSocialiserGenes Gene-based similarity analysis using structured ontologies on functions, diseases, and phenotypes ~70
 xSocialiserSNPs SNP-based similarity analysis using Experimental Factor Ontology on GWAS traits ~60
 xCircos Circos plot of similarity outputs ~10
 xSocialiserDAGplot DAG plot of one set of terms used for similarity analysis <1
 xSocialiserDAGplotAdv DAG plot of two sets of terms used for similarity analysis <1
Network analysis
 xSubneterGenes Gene-based network analysis ~60
 xSubneterSNPs SNP-based network analysis ~60
 xVisNet Network visualisation <1
  1. aRuntime (measured by seconds) tested using one core on Mac OS X
  2. bIncluding structured ontologies on functions, diseases, and phenotypes, and non-structured ontologies on pathways, regulatory/expression signatures, druggability, structural domains, GTEx eGene tissues, others
  3. cIncluding genomic annotations sourced from ENCODE, FANTOME5, BLUEPRINT Epigenome, Roadmap Epigenomics, The Cancer Genome Atlas, UCSC, others