Provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.

Computes proximity between rows or columns of large matrices efficiently in C++.
    Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries.
    Among various built-in similarity/distance measures, computation of correlation,
    cosine similarity, Dice coefficient and Euclidean distance is particularly fast.

Determine minimal protein set explaining
    peptide spectrum matches. Utility functions for creating fasta amino acid databases with decoys and contaminants.
    Peptide false discovery rate estimation for target decoy search results on psm, precursor, peptide and protein
    level. Computing dynamic swath window sizes based on MS1 or MS2 signal distributions.

Utilize the Bayesian prior and posterior predictive checking
   approach to provide a statistical assessment of replication success 
   and failure. The package is based on the methods proposed in 
   Zhao,Y., Wen X.(2021) <arXiv:2105.03993>.

Provides a function to convert 'PRQL' strings to 'SQL' strings.
    Combined with other R functions that take 'SQL' as an argument,
    'PRQL' can be used on R.

Reverse depends for a given package are queued such that multiple
 workers can run the reverse-dependency tests in parallel.

Computes the areas under the precision-recall (PR) and ROC curve for weighted (e.g., soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method. References: Davis and Goadrich (2006) <doi:10.1145/1143844.1143874>; Keilwagen et al. (2014) <doi:10.1371/journal.pone.0092209>; Grau et al. (2015) <doi:10.1093/bioinformatics/btv153>.

Tests periodicity in short time series using response surface regression.