annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

Gaonkar, Krutika S.; Marini, Federico; Rathi, Komal S.; Jain, Payal; Zhu, Yuankun; Chimicles, Nicholas A.; Brown, Miguel A.; Naqvi, Ammar S.; Zhang, Bo; Storm, Phillip B.; Maris, John M.; Raman, Pichai; Resnick, Adam C.; Strauch, Konstantin; Taroni, Jaclyn N.; Rokita, Jo Lynne

doi:10.1186/s12859-020-03922-7

BMC Bioinformatics

Table 1 Available fusion annotation and prioritization tools

From: annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

Tools	Software implementation	Compatible fusion algorithms	Annotations	Prioritization	Visualization	Code availability	Last Updated
annoFuse	R	Arriba, STAR-Fusion for annoFuse; agnostic for shinyFuse	Protein Domains, Kinase, Transcription Factor, Oncogene, Tumor Suppressor Gene, Kinase Domain Retention, Reciprocality, CTAT_HumanFusionLib, Gene Homolog, Expression	Based on quality/artifact filtering, functional, and oncogenic annotation	Genomic view of single or multiple fusion events() with domains, Recurrent fusions and recurrently fused genes barplots	https://github.com/d3b-center/annoFuse/	September 2020+
AGFusion	Python	Algorithm agnostic; requires two fusion gene partners (gene symbol, Ensembl ID, or Entrez gene ID), predicted fusion junctions in genomic coordinates, genome build	Protein domains		Amino acid structure of fusion	https://github.com/murphycj/AGFusion	September 2019
chimera	R package	chimeraScan, bellerophontes, deFuse, FusionFinder, FusionHunter, mapSplice, tophat-fusion, FusionMap, STAR, Rsubread, fusionCatcher		Uses Oncofuse to prioritize oncogenic fusions		https://rdrr.io/bioc/chimera/	March 2015
chimeraviz	R package	deFuse, EricScript, InFusion, JAFFA, FusionCatcher, FusionMap, PRADA, SOAPFuse, STAR-Fusion			Genomic view of fusion event (Breakpoints required)	https://github.com/stianlagstad/chimeraviz	October 2019
co-Fuse	R	FusionCatcher, SoapFuse, TopHat, DeFuse		Recurrence detection		https://github.com/sakrapee/co-fuse	May 2017
FusionAnnotator	perl	Algorithm agnostic; requires fusion gene partners	CTAT_HumanFusionLib, Gene Homolog			https://github.com/FusionAnnotator/FusionAnnotator	July 2019
FusionHub	web-based	Algorithm agnostic; requires fusion gene partners to search databases for fusion and uses breakpoints from ChimerSeq to visualize		Utilizes oncofuse for oncogenicity	Circos, domain, network view of fusions	https://fusionhub.persistent.co.in/	June 2018
FusionPathway	R	Algorithm agnostic; Fusion gene Entrez IDs and gene symbols, Pfam protein domain IDs of parental genes		Oncogenic pathway association using GSEA		https://github.com/perwu/FusionPathway/	September 2019
Oncofuse	Java/Groovy	Tophat-fusion and TopHat2, FusionCatcher, RNASTAR	Protein domains, expression	Bayesian probability of oncogenicity		https://github.com/mikessh/oncofuse	February 2016
Pegasus	Java/Perl/Python/Bash	chimerascan 0.4.5, defuse 0.4.3, bellerophontes 0.4.0	Kinase, Protein domains	Driver Score for oncogenicity		https://github.com/RabadanLab/Pegasus	February 2016
confFuse	Python	deFuse		Feature dependent scoring		https://github.com/Zhiqin-HUANG/confFuse	November 2017

List of ten openly-available fusion annotation and prioritization software tools, compared to annoFuse. Only AGFusion, FusionAnnotator, Fusion Pathway, and certain functions of FusionHub are algorithm agnostic, and most algorithms require outdated fusion algorithm input

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ISSN: 1471-2105

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