A joint mixture model has been developed by Majumdar et al. (2025) <doi:10.48550/arXiv.2412.17511> that integrates information from gene expression data and methylation data at the modelling stage to capture their inherent dependency structure, enabling simultaneous identification of differentially methylated cytosine-guanine dinucleotide (CpG) sites and differentially expressed genes. The model leverages a joint likelihood function that accounts for the nested structure in the data, with parameter estimation performed using an expectation-maximisation algorithm.

A toolkit for detecting Differential Item Functioning (DIF) 
    using Logistic Regression (LR) as described in Swaminathan and Rogers 
    (1990) <doi:10.1111/j.1745-3984.1990.tb00754.x>, the IRT Likelihood Ratio Test 
    (LRT) following Thissen, Steinberg & Wainer
    (1993, ISBN:0-8058-0972-4), and model-based recursive partitioning 
    (MOB) as implemented in 'strucchange' following Strobl, Kopf and Zeileis 
    (2015) <doi:10.1007/s11336-013-9388-3>. Designed for both standard two-group 
    and intersectional multi-group designs, 'iDIFr' prioritises effect size 
    reporting alongside statistical significance, clear guidance on group 
    construction, and interpretable output suitable for applied testing 
    contexts. Built-in Intersectional Contrast Analysis (ICA) classifies 
    items as amplified, pure-intersection, obscured, or none by comparing 
    single-variable and intersectional analyses.

Fits covariate dependent partial correlation matrices for integrative models to identify differential networks between two groups. The methods are described in Class et. al., (2018) <doi:10.1093/bioinformatics/btx750> and Ha et. al., (2015) <doi:10.1093/bioinformatics/btv406>.

Plot idiograms of karyotypes, plasmids, circular chr. having a set of data.frames for chromosome data and optionally mark data. Two styles of chromosomes can be used: without or with visible chromatids. Supports micrometers, cM and Mb or any unit. Three styles of centromeres are available: triangle, rounded and inProtein; and six styles of marks are available: square (squareLeft), dots, cM (cMLeft), cenStyle, upArrow (downArrow), exProtein (inProtein); its legend (label) can be drawn inline or to the right of karyotypes. Idiograms can also be plotted in concentric circles. It is possible to calculate chromosome indices by Levan et al. (1964) <doi:10.1111/j.1601-5223.1964.tb01953.x>, karyotype indices of Watanabe et al. (1999) <doi:10.1007/PL00013869> and Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes by morphology Guerra (1986) and Levan et al. (1964).