TranscriptoScope Windows v0.4.9

TranscriptoScope v0.4.9 adds a standalone Windows installer while preserving the application and analytical behavior from v0.4.8.

Recommended download:

• TranscriptoScope_Windows_Store_v0.4.9.exe is the easiest installation option. It bundles R 4.6.0 and the required R/CRAN/Bioconductor package library, so a separate R installation is not required.
• TranscriptoScope_Windows_v0.4.9.zip remains available as the smaller manual-install alternative for users who already have R.

Installer validation:

• Built with Inno Setup 6.7.3 for x64-compatible Windows systems.
• Bundles 107 package dependencies, including DESeq2, fgsea, WGCNA, Shiny, ggplot2, and readxl.
• Installed successfully for the current user under a path containing spaces.
• Passed the bundled package preflight using only the private R runtime and private package library.
• Passed the complete developer smoke analysis for raw counts, normalized expression, fold-change modes, ORA, ranked pathway analysis, and WGCNA.
• Launched the local Shiny application successfully and reported version 0.4.9.
• Uninstalled cleanly.
• Contains no KEGG cache files and no development log files.

Important Windows note:

• The EXE is not currently code-signed. Windows SmartScreen may show an unknown-publisher warning. Download it only from this official release and verify the accompanying SHA-256 checksum before running it.

SignPath Foundation code signing:

• TranscriptoScope is applying to the SignPath Foundation open-source code-signing program. If approved, future official Windows installer artifacts will be signed through SignPath Foundation.
• The current v0.4.9 EXE remains unsigned; this notice does not imply that the application has already been approved or that existing release files are signed.

Scientific scope:

• This is a distribution-only release. It does not change the DESeq2, ORA, fgsea, or WGCNA statistical calculations in v0.4.8.
• The analytical workflows retain the validation evidence documented for v0.4.7 and the smoke-tested input/interface improvements released in v0.4.8.

Licensing and resources:

• The MIT license applies to TranscriptoScope source code and project-authored documentation only. Bundled R and package dependencies retain their own licenses.
• KEGG-derived cache files are not bundled. Optional KEGG workflows use user-initiated KEGG REST access and local caching.

Archive:

• Version-specific Zenodo DOI: https://doi.org/10.5281/zenodo.21331626
• Stable all-versions Zenodo concept DOI: https://doi.org/10.5281/zenodo.20659461

TranscriptoScope Windows v0.4.8

TranscriptoScope v0.4.8 improves input handling and refreshes the interface while preserving the validated analytical workflows from v0.4.7.

Highlights:

• Added automatic input-type detection for raw counts, normalized expression, fold-change plus adjusted-p-value tables, and fold-change-only tables.
• Kept ambiguous inputs under manual user control and now explains why the app did not change the selected type.
• Added automatic support for both vertical and horizontal sample-metadata layouts.
• Added direct XLSX/XLS metadata import from the first worksheet.
• Added downloadable vertical and horizontal metadata examples.
• Improved empty states, diagnostic guidance, visual hierarchy, responsive spacing, tabs, forms, buttons, and the application header.

Validation:

• The full end-to-end developer smoke test passed for raw counts, normalized expression, fold-change modes, ORA, ranked pathway analysis, and WGCNA.
• Automatic input-type tests passed for all four supported input categories.
• Vertical and horizontal metadata produced identical aligned metadata for the supplied 12-sample workbooks.
• Store dependency preflight passed with readxl included.
• Package inspection confirmed version 0.4.8 and zero bundled KEGG cache files.
• This release does not change the DESeq2, ORA, fgsea, or WGCNA statistical calculations validated in v0.4.7.

Release notes:

• Built from TranscriptoScope source version 0.4.8.
• The Windows ZIP excludes KEGG-derived cache files. KEGG workflows use optional user-initiated KEGG REST access and local user caching.
• The MIT license applies to TranscriptoScope source code and project-authored documentation only; third-party biological resources and R/Bioconductor packages remain subject to their own terms.
• Excel support applies to sample metadata. Primary count, expression, and fold-change inputs remain CSV, TSV, or TXT.

Archive:

• Zenodo v0.4.8 DOI: https://doi.org/10.5281/zenodo.21329336
• Stable all-versions Zenodo concept DOI: https://doi.org/10.5281/zenodo.20659461

TranscriptoScope Windows v0.4.7

TranscriptoScope v0.4.7 expands the validated Network Analysis workflow and its reproducibility exports.

Highlights:

• Added sample-clustering dendrogram output before network interpretation.
• Added scale-free topology fit and mean-connectivity plots plus the underlying candidate-power table.
• Added a gene dendrogram with aligned module-color annotation.
• Added downloadable module-size and module-trait heatmap PNG files.
• Added module enrichment against the current upregulated, downregulated, and combined DEG sets.
• Added six WGCNA CSV tables and five Network Analysis PNG files to the result bundle.
• Extended the exported R rerun script to reproduce scale-free topology and module-enrichment tables.

Validation:

• Core analytical validation passed 71/71 checks and 11/11 protocol items in two fresh R sessions.
• The two core sessions produced identical analytical observations after run metadata was excluded and 12/12 byte-identical saved analytical artifacts.
• VP-16 feature-extension validation passed 14/14 checks.
• Expanded VP-17 WGCNA/Network Analysis validation passed 19/19 checks.
• VP-17 independently verified sample clustering, scale-free topology, gene dendrogram/module colors, module enrichment, all six WGCNA tables, all five network plots, UI/download contracts, result-bundle contents, and reproducibility reruns.
• The end-to-end developer smoke test passed from both the source tree and the packaged ZIP extracted under a path containing spaces.
• Package inspection confirmed version 0.4.7, inclusion of the public VP-17 evidence note, and zero bundled KEGG cache files.

Release notes:

• Built from TranscriptoScope source version 0.4.7.
• The Windows ZIP excludes KEGG-derived cache files. KEGG workflows use optional user-initiated KEGG REST access and local user caching.
• The MIT license applies to TranscriptoScope source code and project-authored documentation only; third-party biological resources and R/Bioconductor packages remain subject to their own terms.
• WGCNA outputs are exploratory coexpression results and should not be interpreted as causal regulatory relationships.

Archive:

• Zenodo v0.4.7 DOI: https://doi.org/10.5281/zenodo.21291831
• Stable all-versions Zenodo concept DOI: https://doi.org/10.5281/zenodo.20659461

TranscriptoScope Windows v0.4.6

TranscriptoScope v0.4.6 adds the current feature-extension build used for VP-16 and VP-17 validation.

Highlights:

• Advanced DESeq2 design controls for additive adjustment factors, condition-by-factor interaction designs, interaction coefficients, condition effects within interaction levels, and custom resultsNames() coefficients.
• Reproducibility bundles now record fitted DESeq2 formulas, contrast modes, result names, interaction settings, analysis-ready inputs, and rerun code.
• User-facing diagnostics now explain common upload and workflow failures with concrete repair steps.
• Downloadable example input templates are included for counts, metadata, normalized expression, fold-change tables, and custom gene sets.
• ORA and GO DAG displays now handle duplicate labels and non-GO enrichment results more gracefully.
• Pathway cnetplot labels are cleaner, the plotted network area is larger, and high-resolution TIFF export is available.
• The top-level Refresh control now clears result/error state before reload.

Release notes:

• Built from TranscriptoScope source version 0.4.6.
• The Windows ZIP excludes KEGG-derived cache files. KEGG workflows use optional user-initiated KEGG REST access and local user caching.
• The MIT license applies to TranscriptoScope source code and project-authored documentation only; third-party biological resources and R/Bioconductor packages remain subject to their own terms.

Validation summary:

• R syntax parse checks passed for the updated R source files.
• Release ZIP inspection confirmed bundled version 0.4.6.
• Release ZIP inspection confirmed no bundled *_kegg.csv cache files.

TranscriptoScope Windows v0.4.5

TranscriptoScope Windows v0.4.5

This release adds the pathway and network-analysis features added after v0.4.4.

Zenodo DOI

• Version DOI: https://doi.org/10.5281/zenodo.20824250
• Concept DOI: https://doi.org/10.5281/zenodo.20659461

What's new

• Added TF.Target.GTRD as a built-in pathway database option for both enrichment and ranked pathway analysis.
• Added a Network Analysis tab with WGCNA module summaries, module-trait correlations, gene-module assignments, eigengenes, CSV downloads, and result-bundle exports.
• Added pathway cnetplot rendering, PNG export, cnetplot edge CSV export, and result-bundle outputs.
• Updated pathway cnetplot gene labels to prefer readable gene symbols over systematic gene identifiers when annotation is available.
• Added GO DAG plotting for over-represented GO terms, including ontology-derived ancestor relationships, significance-level coloring, PNG export, node and edge CSV exports, and bundle outputs.
• Added offline GO ontology relationship tables and reproducible scripts for rebuilding bundled gene-set and DAG resources.

Validation

• Smoke test passed on Windows using the bundled/runtime Rscript.
• Optional KEGG REST smoke test was skipped unless TRANSCRIPTOSCOPE_TEST_KEGG=1 is set.

SHA256

51EA3C2B8932BCF2F125A1D4CE2F6E04515E5E069CE02901C66884B91309140D  TranscriptoScope_Windows_v0.4.5.zip

TranscriptoScope Windows v0.4.4

TranscriptoScope Windows v0.4.4

This patch release updates the public Windows/Shiny app package with interface and pathway-export improvements added after v0.4.3.

What's new

• Added a top-level Refresh button that reloads the current Shiny session.
• Added Significant Pathways CSV for ranked pathway-analysis results below the selected pathway FDR cutoff.
• Added Top Plotted Pathways CSV, exporting the same pathway subset shown in the Top Pathways plot.
• Added pathway_significant_pathways.csv and pathway_top_plotted_pathways.csv to the result bundle when pathway analysis has been run.
• Shared the top-pathway selection logic between plotting and CSV export so displayed and downloaded pathway subsets match.

Resource and licensing notes

• TranscriptoScope source code and project-authored documentation are MIT licensed.
• The public release does not redistribute KEGG-derived pathway cache CSV files.
• KEGG pathway use is optional and user initiated through KEGG REST with local user caching.
• Third-party biological resources and R/Bioconductor packages remain governed by their own licenses and citation requirements.

Validation

• app.R parse/source check passed.
• scripts/smoke_test.R passed using R 4.6.0.
• Release ZIP was rebuilt after excluding generated outputs/ and work_logs/ folders.

Files

• TranscriptoScope_Windows_v0.4.4.zip
• TranscriptoScope_Windows_v0.4.4.sha256

SHA256:

F90B355F452731205F256D43F393B4C814340115DA85058708E3F7AA6C003C36  TranscriptoScope_Windows_v0.4.4.zip

TranscriptoScope Windows v0.4.3

TranscriptoScope Windows v0.4.3

TranscriptoScope is a Windows-friendly local Shiny application for differential gene expression analysis, functional enrichment, and ranked pathway analysis.

Download

Download TranscriptoScope_Windows_v0.4.3.zip from this release, extract it, and run:

Install_TranscriptoScope.bat

After installation, launch TranscriptoScope from the Desktop or Start Menu shortcut.

What This Release Includes

• Raw read-count analysis with DESeq2.
• Normalized expression analysis for decimal-valued expression matrices.
• Fold-change table import modes.
• PCA, volcano, MA, and regulation-summary plots.
• ORA enrichment with bundled organism resources.
• Rosby's Lab-style ORA, defined as protein-coding directional ORA.
• Ranked pathway analysis with fgsea.
• Bundled example data, annotation resources, and Windows install scripts.

Changes In v0.4.3

• Made Windows package installation explicitly non-interactive by forcing binary package installs and suppressing source-package prompts.
• Added package-install progress messages for cleaner Windows runtime validation.

Validation

The manuscript validation package reports:

• 71 of 71 core checks passed for TranscriptoScope 0.4.2 statistical workflows.
• VP-14 Windows deployment validation passed with the repaired 0.4.3 Windows package in a clean Windows 11 standard-user environment and a separate true-offline launch test after dependency setup.

Checksum

SHA256  TranscriptoScope_Windows_v0.4.3.zip  0148DB0BE366AB573BBC13BE038C2545B1F16C7AECCAA4F0F05A69439732F37E

Citation

If you use TranscriptoScope in research, cite this software release and cite the underlying methods/packages used in your analysis, including DESeq2 for differential expression and fgsea for ranked pathway analysis.

Release DOI: 10.5281/zenodo.20659462

Important Notes

This is a research software tool. Users are responsible for reviewing outputs, choosing appropriate statistical settings, and following institutional policies for sensitive or protected datasets.

Microsoft Store Candidate Installer

A Store-style .exe installer is available for Microsoft Partner Center testing and submission preparation:

ext TranscriptoScope_Windows_Store_v0.4.3.exe SHA256 80E49ABAF1590AE3735B62B24BFDA8F5BB5317968CCFD7719EBA3FBC46BE73BA

This installer bundles R 4.6.0 and the required R package library for offline installation. Local host testing passed install, bundled package preflight, local Shiny launch, and uninstall checks. Final Microsoft Store submission should wait for a clean Windows 11 VM install/launch pass and true offline VM pass.