annoFuse v0.91.0 (released 2022-09-26)

New features

Add capability for annotation of custom fusion input file with minimal required columns
Add custom type annotation that checks for required columns and maps input columns to output columns using config file
Update fusion standardization function to accept custom fusion input that checks for few required columns
Config file is optional and can be use to map input columns with output columns
Custom fusion input type was built on top of existing STAR-Fusion and Arriba fusion framework.
This version will continue to support both existing caller types with same implementation

shinyFuse, a shiny app for interactive exploration of fusions from annoFuse prioritization
reportFuse, a reproducible R Mardown notebook for fusion analysis using annoFuse
Technical validation vignette using TCGA fusion calls
Add functionality to visualize fusion breakpoints by fusion or by sample, in addition to viewing breakpoints for a specific fusion for all samples in a cohort
Add breakpoint plots for 5'-fused gene, 3'-fused gene, in addition to plotting both genes
Update all functions to snake_case
Add breakpoint location (genic, intergenic, or intragenic) to standardFusioncalls
Add SpanningDelta to standardFusioncalls
Add reciprocal status for kinase fusions
Update OpenPBTA data from release-v14-20200203 to release-v16-20200320
Add col_type reading function for STAR-Fusion and Arriba
Add function examples
Add project-specific fusion filtering example
Make kinase domain as default for checkDomainStatus

Remove ConjoinG filter to capture known true positive reciprocal fusion FIP1L1--PDGFRA discovered in OpenPBTA vignette
Change default SpanningDelta filter from 10 to 100 based on TCGA validation
Update frameshift domain retention to "Yes" when breakpoint occurs after kinase domain in Gene1A (5' gene)
Update plot text sizing