Changelog

Source: NEWS.md

CLAMP 0.99.11

Bug fixes

• Kept a single documentation URL in DESCRIPTION to avoid a merged hyperlink on the Bioconductor package page.
• Replaced unavailable Bioconductor release badges with “Not yet released” and clarified installation from Bioconductor devel in the README.

CLAMP 0.99.10

Improvements

• Updated the package hex logo to use a fully opaque hexagon background and refreshed man/figures/clamp.png and man/figures/logo.png accordingly.

CLAMP 0.99.8

Bug fixes

• Fixed whole-blood examples in the introductory vignette and README to use the supplied normalized expression values directly, avoiding redundant CPM normalization and log2 transformation that caused the pkgdown build to fail during CLAMPfull().

CLAMP 0.99.7

Improvements

• Added log2_transform = TRUE to preprocessCLAMP(), preprocessCLAMPFBM(), and cleanFBM(). Set it to FALSE to skip log2 transformation while retaining missing-value handling and filtering.

Bug fixes

• Changed preprocessCLAMP() to use population variance, matching preprocessCLAMPFBM() for variance filtering and downstream scaling.

CLAMP 0.99.6

Bug fixes

• Corrected the pathway dot-plot heading and Visualization examples in the introductory vignette so all six plots are rendered.

CLAMP 0.99.5

Improvements

• Added automated BiocCheck and cross-platform R CMD check workflows.
• Added automatic pkgdown deployment after updates to devel.

CLAMP 0.99.4

Bug fixes

• Made preprocessCLAMP() conditionally log2-transform and replace missing values before filtering, matching preprocessCLAMPFBM().
• Made CLAMPplotU() handle missing FDR values when no pathways pass the requested thresholds.

CLAMP 0.99.0

New features

• Initial Bioconductor submission.
• Implements prior-informed latent variable decomposition for gene expression.
• Supports file-backed matrices (bigstatsr::FBM) for large datasets.
• Added CPM, z-score, and filtering functions for preprocessing.
• Projection of new datasets into pre-trained models.
• Vignettes with example workflows and detailed documentation.

Improvements

• Optimized in-place operations for large matrices.
• Added cross-validation utilities and adaptive sparsity support.
• Roxygen2 documentation for all exported functions.

Bug fixes

• Fixed edge case in CPM normalization for zero-count columns.
• Corrected NA handling in preprocessing.