CHANGES IN VERSION 0.99.5

- New Features: Added countReadsSingleCell() and helper functions to enable 
single-cell Ribo-seq read counting.

CHANGES IN VERSION 0.99.4

- New Features: Added seqlevels_style and bam_output_dir arguments to 
getExonicReads() to enable chromosome renaming and custom output directory.

- Bug Fixes: Added writhr to DESCRIPTION and fixed vignette.


CHANGES IN VERSION 0.99.3

- BAM filtering: Introduced getExonicReads() for extracting exonic reads from 
BAM files.

- Improved unit test coverage: Added more tests and achieved 81% coverage.

- Improved clarity: Renamed DOTSeqDataSetsFromSE() to 
DOTSeqDataSetsFromFeatureCounts() for alignment with input type.


CHANGES IN VERSION 0.99.2

- Vignette Improvement: Expanded documentation now demonstrates the use of 
getORFs(), countReads(), and DOTSeqDataSetsFromSE() with the 
pasillaBamSubset package.


CHANGES IN VERSION 0.99.1

- Simulation Enhancements: The simDOT() function now returns a DOTSeqDataSets 
object, providing a structured container for simulated data and improving 
downstream compatibility.

- Improved Plotting: Plot functions now dynamically adjust margins and panel 
sizes for better layout.


CHANGES IN VERSION 0.99.0

- Unified Workflow: The DOTSeq() wrapper function provides a streamlined 
  interface for performing Differential ORF Translation analysis, while also 
  exposing modular steps for advanced customisation.

- Data Structure: SummarizedExperiment is used as the foundational class for 
  organising input data, model outputs, and metadata.

- Bayesian Inference: Differential ORF Usage (DOU) is assessed using adaptive 
  shrinkage via the ashr package, yielding posterior summaries such as 
  PosteriorMean and local false sign rates (LFSR) for robust effect size 
  estimation and uncertainty quantification.