NEWS
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().
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 1.1.7
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 1.1.4
NEW FEATURES
- Added option to scale scores by the maximum value
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 0.99.0
NEW FEATURES
- Added a
NEWS.md file to track changes to the package.