Changes in version 0.99.49 - Step 4 Phenodata Browser: show the full GSE phenodata table immediately (with column list), and run GEO enrich only after the UI flush so the browser and column selector no longer stay blank while NCBI metadata is fetched. Column selection no longer waits on normalization. Changes in version 0.99.48 - Phenodata Browser: skip reactiveValues write-back when enrich does not change the table, and isolate thin-only enrich in renderUI/DT so badge/DT no longer re-enter on every flush (fixes stuck "Columns: 1" after successful enrich). Changes in version 0.99.47 - Phenodata enrich: case-insensitive GSE key write-back so enriched columns update the RNA/micro list the browser actually reads (not a mismatched micro stub). - Replace whole metadata lists when storing enrich results (reactiveValues-safe). - Treat title/geo_accession-only tables as thin; warn when enrich cannot add columns. - Re-enrich thin phenodata lists before setting download_complete so Groups badge/DT see rich columns. Changes in version 0.99.44 - Remove all requireNamespace("rmda") / rmda code paths from the nomogram DCA module (fixes R CMD check WARNING about undeclared dependency). - Normalize NEWS.md section titles to # GExPipe x.y.z so R can parse version history. Changes in version 0.99.43 - Correct co-author names to Naeem Mahmood Ashraf and Prof. Dr. Muhammad Farooq Sabar. - Remove unavailable Suggests package rmda (Bioconductor CHECK ERROR). Nomogram DCA uses dcurves (already preferred in code). Changes in version 0.99.40 BiocCheck - Rename GSEA map field cat to msig_category so BiocCheck no longer flags a false cat() hit. - Add maintainer ORCID (0000-0003-2646-8106) in Authors@R. Changes in version 0.99.39 Authors - Add co-authors Naeem Mahmood Ashraf and Prof. Dr. Muhammad Farooq Sabar; Safa Rafique remains maintainer (cre). Changes in version 0.99.38 Bioconductor NOTES cleanup - Move optional feature packages from Imports to Suggests: Boruta, car, cicerone, corrplot, dcurves, kernlab, mixOmics, SHAPforxgboost (use requireNamespace guards). - Prefer seq_len/seq_along; replace cat()/redundant stop-warn prefixes in Shiny servers. - Treat Suggests packages as optional during attach/bootstrap (core Imports remain required). Changes in version 0.99.37 Package hygiene - Exclude and untrack GExPipe(original_paper)/ from the Bioconductor package tree (.Rbuildignore + .gitignore). Changes in version 0.99.36 SPB NOTES cleanup (reviewer request) - Expand NAMESPACE importFrom for grDevices/graphics/stats/utils/shiny/ggplot2/DT/grid. - Expand utils::globalVariables() for NSE column names and Shiny symbols. - Replace sapply() with vapply(); prefer seq_len() / sample.int(). - Replace ggplot print(p) with returning p in renderPlot. - Remove <<- via env boxes / reactiveValues assignment. - Fix gexp_fetch_geo_series_matrix_metadata call in validation server. Changes in version 0.99.35 Bioconductor check warnings - Replace non-ASCII characters in R/ with ASCII equivalents. - Declare Suggests: bslib, crosstalk, devtools, fontawesome, htmltools, htmlwidgets, rmda. - Replace set.seed() with withr::local_seed() / withr::with_seed() (BiocCheck). Changes in version 0.99.34 SPB / R CMD check - Fix gexp_qc_build_sample_dataset_map man page example matrix dimensions. Changes in version 0.99.33 Documentation - Clarify gexp_align_rnaseq_sample_names() runs after GEO download (GSE ID workflow), not manual data entry; fix example matrix dimensions in man page. Changes in version 0.99.32 SPB / R CMD check - Regenerate man/gexp_align_rnaseq_sample_names.Rd example (fixes examples ERROR). Changes in version 0.99.31 SPB / R CMD check fixes - Fix gexp_align_rnaseq_sample_names() example matrix dimensions. - Skip source-tree-only bioc-review tests when R/ is not in installed layout. - Harden server namespace test; avoid false match on inst/shinyapp/server.R. - Remove install.packages() from GitHub bootstrap (BiocCheck compliance). Changes in version 0.99.30 Tests - Fix test-bioc-review.R shinytest2 readme path for covr / installed-package test runs. Changes in version 0.99.29 Bioconductor second-review response - Vignette: 30 end-user screenshots in vignettes/images/; maintainer-only notes removed. - Step 4: title column fallback for poorly annotated GEO series; optional group rename at Group Summary. - DE/ML contrasts respect custom reference/comparison labels. Changes in version 0.99.28 Shinytest2 readiness signal - Inject shinytest2::use_shinytest2() in test mode so window.shinytest2.ready is set for AppDriver. Changes in version 0.99.27 Shinytest2 GEO download scenario - Added tests: empty GSE validation and GSE ID + Start Processing (GSE62646 by default). - Helpers: .gexpipe_shinytest2_poll_output(), .gexpipe_shinytest2_start_geo_download(). - Added inst/scripts/record-shinytest2-geo.R for interactive recording. Changes in version 0.99.26 Shiny testing (Bioconductor review) - Added shinytest2 workflow tests (tests/testthat/test-shiny-integration.R) and helper-shinytest2.R for welcome → dashboard → QC navigation. - Skip full Bioconductor attach in shiny.testmode so shinytest2 sessions start quickly. - Documented usage in inst/scripts/README-shinytest2.md. Changes in version 0.99.25 Bioconductor review (second round) - Moved Shiny bootstrap from inst/shinyapp/global.R into R/gexpipe_shinyapp_bootstrap.R. - Replaced all suppressWarnings() / suppressMessages() in R/ with targeted quiet I/O helpers. - Added tests/testthat/test-shiny-coverage.R and expanded bioc-review / app-builder tests for UI tabs, utils_shiny_app, and dummy_imports. - Fixed .gexpipe_best_version() for R 4.6+ (package_version comparison). Changes in version 0.99.24 Vignette (Bioconductor review) - Removed maintainer-only text from vignettes/GExPipe.Rmd (screenshot paths, internal vignette notes). - Moved walkthrough screenshots to vignettes/images/ with direct knitr::include_graphics() calls. - Added five PNG figures referenced by the vignette; maintainer regeneration documented in inst/scripts/README-vignette-screenshots.md. Changes in version 0.99.23 Bioconductor review (code organization and testing) - inst/shinyapp/server.R and ui.R now delegate to gexp_app_server() / gexp_app_ui() instead of duplicating modular logic or calling source() on tab modules. - Added gexpipe_spearman_cor() and removed suppressWarnings(cor(...)) from ML plots. - Added tests/testthat/test-coverage-helpers.R for normalization, ID detection, WGCNA prep, download overlap helpers, and UI/ML utilities. Changes in version 0.99.22 Bioconductor review (testing and code organization) - Added tests/testthat/test-pipeline-helpers.R for download/QC/classify helpers and namespace-based server wiring. - Replaced scattered suppressMessages(capture.output(getGEO...)) with .gexpipe_geo_quiet() and centralized count-file reads in .gexpipe_fread_counts(). - Documented remaining suppression (STRINGdb ID mapping, optional biomaRt chatter). Shiny functional review - Fix generic V2 sample names from headerless GEO count files; per-GSE labels in QC outlier plots before normalization. Changes in version 0.99.21 Bioconductor second review - BugReports now points to GitHub Issues (safarafique/GExPipe). - Shiny server and UI tab modules moved from inst/shinyapp/ to R/ (no runtime source() / custom caching for tab modules). - Added inst/scripts/make-vignette-extdata.R documenting synthetic vignette data. - Removed redundant inst/pkg_versions.txt (versions are in DESCRIPTION). - Reduced suppressWarnings() around namespace unloads; added tests for UI/server builders, helpers, and pipeline wiring. Changes in version 0.99.20