Changes in version 0.1.0                        

  - Standardize the named v5 package logo across README, documentation
    pages and available application headers, with matching light and
    dark artwork.

New features

  - Initial release of bambamR.
  - Data import: bb_read_fastq() and bb_read_bam() with
    ShortRead/Rsamtools or base-R/system-samtools fallback.
  - Quality control: bb_qc(), bb_qc_summary(), and bb_plot_qc() for
    per-read quality, GC content, and read-length distributions.
  - Alignment: bb_align() wrapping STAR, HISAT2, and minimap2.
  - Read counting: bb_count_reads() via GenomicAlignments or
    featureCounts.
  - Normalization: bb_normalize() supporting CPM, TPM (base R), TMM
    (edgeR), and RLE (DESeq2).
  - Differential expression: bb_deseq2(), bb_edger(), and
    bb_limma_voom() returning standardized result data.frames.
  - Visualization: bb_oncoplot(), bb_volcano(), bb_heatmap(), bb_pca(),
    bb_ma_plot() — all return ggplot2 objects.
  - Pipeline orchestrator: bb_pipeline() runs the full analysis from
    FASTQ, BAM, or count matrix to plots in a single call.
  - Export: bb_export_csv(), bb_export_tsv(), bb_export_rds().
  - Shiny app: bb_run_app() launches an interactive analysis dashboard.
  - Example data: bb_example_counts(), bb_example_mutations(), and
    bb_example_de() provide bundled datasets for exploring all features.
  - Two operating modes: minimal (CRAN-only) and full (+ Bioconductor).
    All Bioconductor dependencies are optional and checked at runtime.

Bug fixes

  - None yet.