NEWS
DspikeIn 0.99.28
DspikeIn 0.99.27
DspikeIn 0.99.26
DspikeIn 0.99.25
DspikeIn 0.99.24
DspikeIn 0.99.23
DspikeIn 0.99.22
DspikeIn 0.99.21
DspikeIn 0.99.20
- function added
- reviewer's comments implemented
DspikeIn 0.99.11
- Adding TSE Examples
- Including TSE vignettes
DspikeIn 0.99.10
No major changes recorded.
DspikeIn 0.99.9
- 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.
DspikeIn 0.99.8
Changes
- 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.
DspikeIn 0.99.7
No major changes recorded.
DspikeIn 0.99.6
Changes
- 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.
DspikeIn 0.99.0
Initial submission
- Submitted package to Bioconductor.
- Added spike-in analysis workflows.
- Included synthetic and real microbiome datasets.