Release v0.92.0

Description of changes

This release updatesget_Pfam_domain.R to apply "kinase domain retained" in Gene1B if the fusion is frameshift and the entire domain is retained in the fusion. Previously, this was only assigned as retained if the fusion was inframe.

What's Changed

• Update version by @sakshamphul in #98
• Change get_pfam_domain.R by @zzgeng in #99

New Contributors

• @zzgeng made their first contribution in #99

Full Changelog: v0.91.0...v0.92.0

v0.91.0

Description of changes

Fusion standardization function:

1. This release adds custom type annotation that checks for required columns and maps input columns to output columns using config file.
2. Fusion standardization function has the ability to accept custom type input that checks for few required columns. Config file has been made optionally and can be use to map input columns with output columns. Additionally, it can also be used to generate output columns with specific header name and 'NA' as an entry (Usage: "None" :: "Output_name")
3. Custom type was built on top of existing starfusion and arriba fusion framework. This version will continue to support both of these caller types with same implementation.

Key takeaway:

• 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

What's Changed

• Zenodo badge by @kgaonkar6 in #78
• Added release date for ShinyFuse in the about content section for the… by @federicomarini in #81
• templates for issues and PR by @kgaonkar6 in #79
• Road to bioc + unit-test by @federicomarini in #88
• adding dplyr::one_of by @kgaonkar6 in #82
• Unit test by @kgaonkar6 in #87
• Referring to the new location for the repo of the example data by @federicomarini in #91
• Added citation info about publication to the README file by @federicomarini in #95
• Add custom type annotations by @sakshamphul in #97

Full Changelog: v0.90.0...v0.91.0

v0.90.0

Description of changes

• shinyFuse( ) : web-based application, in the R/Shiny framework, to assist users in performing drill-down operations while interacting with their fusion results. This feature is included in both the annoFuse package as well as a standalone server (http://shiny.imbei.uni-mainz.de:3838/shinyFuse/)

• reportFuse( ) : compiles a full HTML report (using R Markdown) using a template analysis containing multiple summary functions side by side with the code used to generate them. The report can be a valuable means for persistent storage and sharing of results with colleagues.

• TCGA_validation.Rmd : we analyzed a subset of (160) samples from TCGA and compared fusions retained with annoFuse filtering and oncogenic prioritization to those deemed the final call set in a previously published analysis by The Fusion Analysis Working Group PMID: 29617662.

• putative_driver_filtering.Rmd : we demonstrate how to use annoFuse to filter putative oncogenic fusions from a filtered fusion list followed by plotting recurrent fusions, recurrently fused genes, as well as a summary plot.

• function names are now updated to be consistent snake_type

• added features to get_Pfam_domain(),fusion_driver(), annotate_fusion_calls()

v0.2

Description of changes

• This PR adds singleSample run for standardization, red flag filtering using FusionAnnotator and expression based filtering. In addition to the FusionAnnotator annotations the sample calls will also be annotated using the genereferencelist.txt and fusionreferencelist.txt.

• In addition there are functions getPfamDomain() and plotBreakpoint() that add pfam domain information as well as plot breakpoints as shown in vignette.

• In inst/extdata/ test arriba,starfusion and rsem files are availble. We also added RDS files from biomart+pfam dataframe and exons dataframe for domain annotation.

• plotSummary() has plots for retained kinase domains instead of annotation from legacy kinase gene list.

• singleSampleRun.Rmd vignette has been added to display use of annoFuse for sample level analysis.

What does the changes add to package?

Domain level information and ability to run only per sample runs.

v0.1.8

First release of annoFuse