NEWS

DspikeIn 1.3.2

validate_spikein_clade(): fixed the could not find function "DNAStringSet" error in R CMD check (BioC 3.24). Alignment now uses DECIPHER::AlignSeqs() instead of msa::msa(), whose S4 constructor calls DNAStringSet() unqualified and fails when Biostrings is not attached.
validate_spikein_clade(): terminal branch lengths are now matched to the correct tips (previously taken in edge order, not tip order).
validate_spikein_clade(): the reported clade bootstrap is now the support of the sample clade's MRCA node rather than the maximum support in the tree; support is computed on bipartitions because NJ trees are unrooted.
validate_spikein_clade(): edge-length annotations are now drawn with ape::edgelabels() (they were previously drawn on nodes).

validate_spikein_clade(): input validation, unique tip labels, tree rooted on the first reference, plots recorded off-screen (no stray devices or Rplots.pdf), new node_support and branch_table outputs.
Removed the msa dependency (one fewer package in Imports).

No major changes recorded.

Documented both physeq and tse in R/data.R with proper @format, @source, and usage examples.
Fixed system hostname configuration to remove “unknown” from shell prompt.
Verified that vignettes build cleanly and only required doc/ appears in tarball.
Cleaned up redundant or empty directories during build to pass Bioconductor checks.

Streamlined the package by removing non-essential helper and pipeline functions.
Retained core spike-in quantification methods only: validation, scaling, bias correction, and absolute abundance estimation.
Removed dependencies on DESeq2, edgeR, and downstream differential analysis tools.
Updated DESCRIPTION, NAMESPACE, and internal documentation to reflect core-only functionality.
Added clarifying notes in the vignette and package description about the full pipeline availability on the MGhotbi branch.
Reorganized internal structure for improved reproducibility and modular design.
Updated R version dependency to R (>= 4.5.0) to comply with Bioconductor guidelines.
Refined biocViews to match core functionality focus and removed unused categories.

No major changes recorded.

Fixed error caused by missing geom_star() in ggstar.
Updated example sections to conditionally load required packages.
Corrected object reconstruction logic in random_subsample_WithReductionFactor().
Replaced deprecated functions and improved Bioconductor compliance.
Added proper LICENSE formatting to eliminate NOTE.
Documented dataset provenance and processing steps in inst/scripts/data_preparation.md, including SRA BioProject accessions for embedded data.