Includes functions to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot 'XVG' output files from the 'GROMACS' molecular dynamics package.

This toolkit is designed for manipulation and analysis of peptides. It provides functionalities to assist researchers in peptide engineering and proteomics. Users can manipulate peptides by adding amino acids at every position, count occurrences of each amino acid at each position, and transform amino acid counts based on probabilities. The package offers functionalities to select the best versus the worst peptides and analyze these peptides, which includes counting specific residues, reducing peptide sequences, extracting features through One Hot Encoding (OHE), and utilizing Quantitative Structure-Activity Relationship (QSAR) properties (based in the package 'Peptides' by Osorio et al. (2015) <doi:10.32614/RJ-2015-001>). This package is intended for both researchers and bioinformatics enthusiasts working on peptide-based projects, especially for their use with machine learning.

Perform permutation-based hypothesis testing for randomized
    experiments as suggested in Ludbrook & Dudley (1998) <doi:10.2307/2685470>
    and Ernst (2004) <doi:10.1214/088342304000000396>, introduced in Pham et al.
    (2022) <doi:10.1016/j.chemosphere.2022.136736>.

To find the certainty of dominance interactions with indirect
    interactions being considered.

An implementation of two functions that estimate values for percentiles from an ordered categorical variable as described by Reardon (2011, isbn:978-0-87154-372-1). One function estimates percentile differences from two percentiles while the other returns the values for every percentile from 1 to 100.

Several person-fit statistics 
  (PFSs; Meijer and Sijtsma, 2001, <doi:10.1177/01466210122031957>) 
  are offered. These statistics allow assessing whether
  individual response patterns to tests or questionnaires are (im)plausible given 
  the other respondents in the sample or given a specified item response theory model. Some PFSs apply to 
  dichotomous data, such as the likelihood-based PFSs (lz, lz*) and the group-based PFSs 
  (personal biserial correlation, caution index, (normed) number of Guttman errors, 
  agreement/disagreement/dependability statistics, U3, ZU3, NCI, Ht). PFSs suitable to polytomous data include
  extensions of lz, U3, and (normed) number of Guttman errors.