An efficient tool designed for differential analysis of large-scale RNA sequencing (RNAseq) data and Bisulfite sequencing (BSseq) data in the presence of individual relatedness and population structure. 'PQLseq' first fits a Generalized Linear Mixed Model (GLMM) with adjusted covariates, predictor of interest and random effects to account for population structure and individual relatedness, and then performs Wald tests for each gene in RNAseq or site in BSseq.

The quantile varying coefficient model is robust to data heterogeneity, 
    outliers and heavy-tailed distributions in the response variable due to the check
    loss function in quantile regression. In addition, it can flexibly model the dynamic
    pattern of regression coefficients through nonparametric varying coefficient 
    functions. Although high dimensional quantile varying coefficient model has been 
    examined extensively in the frequentist framework, the corresponding Bayesian variable 
    selection methods have rarely been developed. In this package, we have implemented 
    the Gibbs samplers of the penalized Bayesian quantile varying coefficient model with 
    the spike-and-slab priors [Zhou et al.(2023)]<doi:10.1016/j.csda.2023.107808>.
    The Markov Chain Monte Carlo (MCMC) algorithms of the proposed
    and alternative models can be efficiently performed by using the package.

Quantile regression with fixed effects is a general model for longitudinal data. Here we proposed to solve it by several methods. The estimation methods include three loss functions as check, asymmetric least square and asymmetric Huber functions; and three structures as simple regression, fixed effects and fixed effects with penalized intercepts by LASSO.

Quickly and easily generate plots of acoustic data aligned with transcriptions similar to those made in 'Praat' using either derived signals generated directly in R with 'wrassp' or imported derived signals from 'Praat'. Provides easy and fast out-of-the-box solutions but also a high extent of  flexibility. Also provides options for embedding audio in figures and animating figures.