NEWS

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DOTSeq 0.99.8

• Updated CITATION.

DOTSeq 0.99.7

• Improved ID mapping to handle internet connection and BioMart API issues.

DOTSeq 0.99.6

• Added a unit test and an example for countReadsSingleCell().

DOTSeq 0.99.5

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

DOTSeq 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.

DOTSeq 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.

DOTSeq 0.99.2

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

DOTSeq 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.

DOTSeq 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.