Text mining of PubMed Abstracts (text and XML) from <https://pubmed.ncbi.nlm.nih.gov/>.

Easy function for text-mining the 'PubMed' repository based on defined sets of terms.
    The relationship between fix-terms (related to your research topic) and pub-terms (terms which pivot around your research focus)
    is calculated using the pointwise mutual information algorithm ('PMI'). Church, Kenneth Ward and Hanks, Patrick (1990) <https://www.aclweb.org/anthology/J90-1003/>
    A text file is generated with the 'PMI'-scores for each fix-term. Then for each collocation pairs (a fix-term + a pub-term),
    a text file is generated with related article titles and publishing years. Additional Author section will follow in the next version updates.

A set of tools to extract bibliographic content from 'PubMed' database using 'NCBI' REST API <https://www.ncbi.nlm.nih.gov/home/develop/api/>.

Provides various functions for retrieving and
    interpreting information from 'Pubmed' via the API,
    <https://www.ncbi.nlm.nih.gov/home/develop/api/>.

Create a word cloud using the abstract of publications from 'Pubmed'.

'PubTator' <https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/> is a National Center for Biotechnology Information (NCBI) tool that enhances the annotation of articles on PubMed <https://www.ncbi.nlm.nih.gov/pubmed/>. It makes it possible to rapidly identify potential relationships between genes or proteins using text mining techniques. In contrast, manually searching for and reading the annotated articles would be very time consuming. 'PubTator' offers both an online interface and a RESTful API, however, neither of these approaches are well suited for frequent, high-throughput analyses. The package 'pubtatordb' provides a set of functions that make it easy for the average R user to download 'PubTator' annotations, create, and then query a local version of the database.

Finite Gaussian mixture models with parsimonious extended ultrametric covariance structures estimated via a grouped coordinate ascent algorithm, which is equivalent to the Expectation-Maximization algorithm. The thirteen ultrametric covariance structures implemented allow for the inspection of different hierarchical relationships among variables. The estimation of an ultrametric correlation matrix is included as a function. The methodologies are described in Cavicchia, Vichi, Zaccaria (2024) <doi:10.1007/s11222-024-10405-9>, Cavicchia, Vichi, Zaccaria (2022) <doi:10.1007/s11634-021-00488-x> and Cavicchia, Vichi, Zaccaria (2020) <doi:10.1007/s11634-020-00400-z>.