Changelog

Source: NEWS.md

cogeqc 0.99.0

NEW FEATURES

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

cogeqc 1.1.3

NEW FEATURES

• Added a correction for overclustering in calculate_H() that penalizes protein domains in multiple orthogroups.
• Updated vignette to provide a detailed explanation of how homogeneity scores are calculated.

cogeqc 1.1.4

NEW FEATURES

• Added option to scale scores by the maximum value

cogeqc 1.1.7

BUG FIXES

• Variable Duplications_50 of the duplications data frame was not matching variable Dups of the stats data frame in the output of read_orthofinder_stats()

NEW FEATURES

• Replaced dispersal formula with a more meaningful and interpretable one.
• Added a max_size param to plot_og_sizes() to ignore OGs larger than a specific size.

cogeqc 1.1.8

CHANGES

• Synteny assessment formula now also considers scale-free topology fit.

BUG FIXES

• Reference-based orthogroup inference does not require the exact same set of species anymore.

cogeqc 1.3.1

CHANGES

• Added functions to explore assembly and annotation statistics in a context: assembly and annotation stats for NCBI genomes can be extracted through the Datasets API and compared with user-defined values. New functions: get_genome_stats(), compare_genome_stats(), and plot_genome_stats().