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TranscriptoScope Windows v0.5.0

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@Shettima123 Shettima123 released this 17 Jul 08:11
v0.5.0
1060bf0

TranscriptoScope v0.5.0 is the current analytically validated release. It strengthens input safeguards, provenance recording, enrichment universes, ranked-pathway handling, and WGCNA/network analysis while preserving a local, non-admin Windows workflow.

Recommended download

  • TranscriptoScope_Windows_Store_v0.5.0.exe is the easiest option. It bundles R 4.6.0 and 107 required R/CRAN/Bioconductor packages, so users do not need to install R separately.
  • TranscriptoScope_Windows_v0.5.0.zip is the smaller manual-install option for users who already have R.
  • Verify downloads with the matching .sha256 file.

Highlights

  • Adds explicit raw-count provenance confirmation and stronger guards for metadata mismatch, duplicate headers, absent biological replication, and count-matrix misuse.
  • Records the fitted DESeq2 model and statistical settings, including dispersion fit, size-factor method, independent filtering, Cook's cutoff, beta prior, multiple-testing method, and unshrunken log2 fold-change status.
  • Defines standard and protein-coding directional ORA against tested genes eligible for the active resource.
  • Recommends the DESeq2 Wald statistic for count-based ranked pathway analysis and exports duplicate, tie, zero-p-value, and missing-rank diagnostics.
  • Uses the DESeq2 variance-stabilizing transformation for count-workflow WGCNA when available and adds small-cohort, outlier, batch, and topology warnings.
  • Retains advanced interaction contrasts, executable R/Rmd result bundles, vertical/horizontal metadata import, diagnostic guidance, GO DAG/cnetplot exports, and publication-quality TIFF output.

Release verification

  • GitHub Actions installer build: PASS for tag v0.5.0 at commit 1060bf0fae142716e78c3c92adaa3f51d35aa68a.
  • Installed-package preflight on Windows 11: PASS.
  • Full installed application smoke analysis: PASS.
  • Core validation: 71/71 checks and 11/11 protocol items in each of two fresh sessions; saved artifacts were byte-identical.
  • Annotation/resources: 64/64; reproducibility exports: 13/13; advanced designs/features: 15/15; WGCNA: 20/20; input/metadata: 14/14; three-organism case studies: 30/30.
  • Controlled guardrail benchmark: all 15 predeclared scenarios matched their expected outcomes and all 11 acceptance checks passed.

Detailed build and checksum evidence is included in TranscriptoScope_v0.5.0_installer_validation.txt.

Important Windows note

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

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 a local user cache.

Archive

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