NEWS

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LRDE 1.0.4

• Corrected README function names to use hurdle.LRT() and hurdle.Wald.Test().

LRDE 1.0.3

• Improved numerical stability of Hurdle-NB parameter estimation.
• Added safeguards against non-finite likelihood values during BFGS optimization.
• Improved handling of extreme negative binomial parameters and zero-truncation probabilities.
• Added protection against zero or non-finite initial parameter values.
• Improved initialization of group-specific mean parameters in tag-wise dispersion estimation.
• Added probability clipping to prevent infinite logit transformations.
• Improved robustness of tag-wise dispersion estimation for sparse genes and genes with all-zero counts.

LRDE 1.0.1

• Initial Bioconductor submission of LRDE.
• Implements a hurdle negative binomial (Hurdle-NB) model for differential expression analysis of long-read RNA-seq data.
• Includes: - Data preparation (prepareDGE) - Size factor estimation (sizeFactorsEst) - Tag-wise dispersion estimation (tagwiseEst) - Differential expression testing via: * Likelihood Ratio Test (hurdle.LRT) * Wald Test (hurdle.Wald.Test)
• Supports matrix, data.frame, and SummarizedExperiment inputs.