Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) <doi:10.1038/nbt.2999>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.

Helps with quality checks, visualizations 
    and analysis of mass spectrometry data, coming from proteomics 
    experiments. The package is developed, tested and used at the Functional 
    Genomics Center Zurich <https://fgcz.ch>. We use this package
    mainly for prototyping, teaching, and having fun with proteomics data.
    But it can also be used to do data analysis for small scale data sets.

Tools for Natural Language Processing in French and texts from Marcel Proust's collection 
  "A La Recherche Du Temps Perdu". The novels contained in this collection are 
  "Du cote de chez Swann ", "A l'ombre des jeunes filles en fleurs","Le Cote de Guermantes", 
  "Sodome et Gomorrhe I et II", "La Prisonniere", "Albertine disparue", and "Le Temps retrouve".

Calculate posterior joint and conditional probabilities, probability distributions of population frequencies, and information-theoretic measures, by means of Bayesian nonparametric methods. Data imputation is automatic and done in a principled way. Markov-chain Monte Carlo calculations are automatically handled and do not require user supervision. Applications range from statistical estimation and probabilistic hypothesis testing to evidence-based inference and decision making, in a wide range of disciplines from astrophysics to medicine. For more details and examples see for instance Porta Mana et al. (2026) <doi:10.31219/osf.io/8nr56>, Dunson & Bhattacharya (2011) <doi:10.1093/acprof:oso/9780199694587.003.0005>, Lindley & Novick (1981) <doi:10.1214/aos/1176345331>, Bernardo & Smith (2000) <doi:10.1002/9780470316870>, Müller et al. (2015) <doi:10.1007/978-3-319-18968-0>. Requires the packages 'Nimble', 'parallel', 'extraDistr'.