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Changelog

Source: NEWS.md

bulkMAE (development version)

  • Rewrites the README as a landing page with official backend links and one square patchwork gallery of volcano, heatmap, ORA network, and GSEA ridge plots.

bulkMAE 0.4.1

  • Records Fan XingFu as the package author and maintainer.
  • Stops pkgdown reference builds from following GSVA S4 Rd links, and keeps the pkgdown library uncached so a broken magick stack cannot abort the site build.
  • Adds bulkmae_rename() and a vignette/pkgdown copy of the 0.4 naming map so old run_* / infer_* / prepare_* calls fail with an explicit replacement.
  • Runs BiocCheck on main.
  • Documents installation from the GitHub Release tag or attached source tarball, and keeps portability, full-backend, and coverage off pull requests.

bulkMAE 0.4.0

  • Replaces mixed run_*, infer_*, prepare_*, and backend-specific naming with discoverable <family>_<method>() / <family>_<operation>() APIs.
  • Organizes public functions under mae_*, qc_*, reduce_*, de_*, enrich_*, score_*, activity_*, cluster_*, coexpr_*, network_*, deconv_*, surv_*, ml_*, meta_*, and drug_* families.
  • Consolidates GO, KEGG, and Reactome ORA/GSEA combinations behind explicit method arguments instead of multiplying function names.
  • Removes old exported aliases intentionally so autocomplete exposes one coherent API; an installed migration map records every breaking rename.
  • Restores compatibility across the declared R 4.4+ dependency range, including edgeR tximport/differential-splicing fallbacks, current dream moderation, timeROC namespace resolution, decoupleR method-argument conventions, and namespace-only NMF, WGCNA, MuSiC, and immunedeconv execution.
  • Adds explicit MAE assay/feature helpers and direct TPM normalization from gene lengths stored in rowData, an aligned assay, or a supplied vector/matrix.
  • Completes a simulated-data suite spanning all 84 public functions, including real offline xCell, MuSiC, BayesPrism, NMF, WGCNA, GO, and Reactome backend smoke tests without requiring network services.
  • Keeps network-backed tests disabled by default. Set BULKMAE_RUN_ONLINE_TESTS=true only when deliberately testing remote resources.
  • Extends the standard ggplot2 layer with statistically faithful GSEA classic/ridge plots and ORA bubble/community/radial plots. These views keep rank vectors, ORA ratios, enriched-feature membership, community Jaccard overlap, and radial shared-feature counts distinct instead of coercing them into one generic effect. ORA views reproduce the reference term-specific community nodes, unique radial nodes, compact adj p legend, and white publication backgrounds.
  • Adds a concise executable Chinese airway enrichment tutorial covering method selection, native GO ORA/GSEA results, and all five enrichment plots.

bulkMAE 0.3.0

  • Enforces name-aware sample, design, feature, and annotation alignment across stateless adapters, with early failures for missing covariates and aliased fixed-effect designs.
  • Completes the edgeR quasi-likelihood workflow with dispersion estimation and repairs logical-vector handling in goseq.
  • Strengthens maSigPro, differential-splicing, DCA, consensus clustering, WGCNA, module-preservation, embedding, activity, clinical, and deconvolution input contracts.
  • Keeps WGCNA’s automatic bad-sample/bad-gene filtering while reporting and retaining the quality decision in its native result list.
  • Localizes wrapper-controlled random seeds so calls do not mutate the user’s global random-number stream.
  • Adds executable local examples, conditional backend tests, installed audit guides, and package-level help needed for a standard source build.

bulkMAE 0.2.0

  • Adds a general decoupleR adapter covering enrichment-style and network-aware statistics, resource discovery, and consensus scoring.
  • Adds KEGG/Reactome ORA and GSEA, CAMERA/FRY/mroast, and singscore.
  • Adds consensus-clustering diagnostics, differential co-expression, and WGCNA module preservation.
  • Adds continuous-expression limma, differential splicing, and maSigPro time-course modelling.
  • Adds UMAP/t-SNE, limma batch removal, Kaplan-Meier, and time-dependent ROC.
  • Expands the tutorial and official-source audit map for every new adapter.

bulkMAE 0.1.0

  • Establishes the stateless MAE-to-native-backend contract.
  • Adds import, annotation, QC, preprocessing, differential expression, enrichment, network, deconvolution, and clinical adapters.
  • Adds a complete walkthrough, official-source audit map, and review checklist.