cancereffectsizeR v2.10.1

Minor fixes.

cancereffectsizeR v2.10.0

Tweaked optimizer settings for epistatic inference to improve convergence; added plot_epistasis() and lift_bed(); other minor improvements.

cancereffectsizeR v2.9.0

New visualization function (plot_mutational_signature_effects), and a tweak to how signature effects are calculated in cohorts (sample-level results remain the same). When used with the new ces.refset.hg38 v1.3.0, this release adds prioritization of canonical transcripts in default variant annotations.

cancereffectsizeR v2.8.1

Small fixes and improvements.

cancereffectsizeR v2.8.0

Visualize cancer effects in a variety of ways with plot_effects(), and generate PathScore input files with make_PathScore_input().

cancereffectsizeR v2.7.0

Added mutational_signature_effects() and revamped epistatic inference output.

cancereffectsizeR v2.6.5

Tweak to nonsilent variant option in pairwise gene epistasis function. Also, epistatic output now optionally includes fitted models for exploration.

cancereffectsizeR v2.6.4

Various improvements and minor fixes. See NEWS for more.

cancereffectsizeR v2.6.3

Added VCF reader function vcfs_to_maf_table(), improved user guidance in get_TCGA_project_MAF(), and removed sequential model pending methodology improvements.

cancereffectsizeR v2.6.2

Minor improvements.