Fits the Piecewise Exponential distribution with random time grids using the clustering structure of the Product Partition Models. Details of the implemented model can be found in Demarqui et al. (2008) <doi:10.1007/s10985-008-9086-0>.

Estimate best fit distributions and do power analysis for hypothesis tests on phosphopeptide abundance data.

A PEP, or Portable Encapsulated Project, is a dataset that
    subscribes to the PEP structure for organizing metadata. It is written using
    a simple YAML + CSV format, it is your one-stop solution to metadata
    management across data analysis environments. This package reads this
    standardized project configuration structure into R.
    Described in Sheffield et al. (2021) <doi:10.1093/gigascience/giab077>.

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.

The Pequod colour palette, named after the whaler in
    Herman Melville's Moby-Dick. Provides the full Log base scale
    from warm paper (Log 50) to deep ink (Log 950), eight crew
    accent hues with light and dark variants, and 'ggplot2' scales
    for discrete and continuous mapping. Designed for long-form
    reading and code, with low saturation and a consistent earth-
    pigment register. Full design rationale and accessibility notes
    at <https://tiagojct.eu/projects/pequod/>.