NEWS

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RBPEqBind 0.99.4

Enhancements & Refactoring

• Idiomatic Parallel Architecture: Refactored simulateGrid(), simulateBindingFasta(), and simulateGridFasta() to adhere strictly to the future framework by delegating concurrency to the user-configured future::plan(), running sequentially by default in compliance with Bioconductor guidelines.
• Clean Imports: Cleaned up jsonlite roxygen imports in R/export.R, removing unused stream_out and toJSON.
• Deterministic Visual Testing: Implemented deterministic test fixtures and visual snapshot testing with vdiffr across all plotting routines.

RBPEqBind 0.99.3

Reviewer Remediation & Numerical Hardening

• Harmonized JSON export across aggregated and unaggregated formats.
• Integrated rtracklayer::export.bed for BED file export.
• Replaced linear solver with scale-invariant log-space root-finder in solveEquilibrium().
• Fixed whole-transcript edge background calculation in callPeaks(method = "local").
• Documented raw dataset provenance in inst/scripts/get_extdata.R.

RBPEqBind 0.99.0

Initial Submission Features

• Competitive binding simulation for N RBPs on RNA using equilibrium model
• Concentration grid sweeps for parameter exploration
• FASTA file support for transcriptome-wide binding analysis
• Peak calling with callPeaks()
• Visualization suite: viewModel(), plotBinding(), plotHeatmap(), plotGrid()
• Export tools: exportResults(), exportBed(), makeSE()