NEWS.md

In d3b-center/annoFuse: annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

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

annoFuse v0.90.0 (released 2020-09-18)

New features

• 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

Bug fixes

• 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

Other notes

• Added a NEWS.md file to track changes to the package.

d3b-center/annoFuse documentation built on Oct. 2, 2024, 4:17 a.m.