GeneFox

Reference

Free

Explore public cancer transcriptomes with expression plots, survival analysis, sample PCA, heatmaps, signatures, and on-device statistics. GeneFox explores public gene-expression and survival data from TCGA, NCBI GEO, GTEx, UCSC Xena, Treehouse, and CCLE. Statistics and visualizations run on your device; requests fetch only what your analysis needs. Built for scientists who work with gene-expression data — no coding required. WHAT YOU CAN DO • Browse 65 supported TCGA/NCI Genomic Data Commons cohorts with case counts, sites, disease types, and demographics. • Plot cohort gene expression as box, bar, or strip charts, stratified by clinical variables, subtype, sample type, or mutation status. • Split any of those plots by a second variable for a side-by-side descriptive comparison; reported statistics stay with the single-variable view. • Generate Kaplan–Meier curves with median summaries, log-rank p-values, and—where applicable—Cox High-vs-Low hazard ratios, 95% CIs, and proportional-hazards warnings. • Compare tumor vs. adjacent-normal and matched GTEx normal tissue via the UCSC Xena TOIL hub, with effect sizes and Mann–Whitney U statistics. • Explore 933 Treehouse CCLE v1 cell lines, grouped by TCGA acronym, tissue, disease, histology, or subtype. • Browse independent pediatric and rare-tumor cohorts from UCSC Treehouse, drawn from studies outside TCGA and TARGET. • Chart differential expression as an interactive volcano plot — expression or mutant-vs-wild-type contrasts — with panel-wise Benjamini–Hochberg FDR correction. • Render gene-panel heatmaps with hierarchical clustering, annotation strips, Z-normalization, and an outlier-resistant color scale. • Run Sample PCA (PC1/PC2) using up to 2,000 selected or top-variable genes, for GEO datasets and TCGA cohorts. • Score custom signatures or 41 curated presets from MSigDB, Reactome, and WikiPathways, plus the Wagle et al. 2018 MPAS panel. • Search NCBI GEO Series with cancer-term expansion. Supports series matrices, human NCBI-generated counts, complete-cohort ARCHS4 raw counts for GEO-classified human/mouse expression RNA-seq, and compatible supplementary matrices. • Capture charts in Report Builder and export a multi-figure report with an auto-generated methods section. ASK GENEFOX Ask questions in plain language. Local interpretation runs first; optional Cloud Assist sends only its disclosed interpretation payload after one-time or standing consent. Scientific analyses stay on-device. PRIVACY GeneFox has no ads, behavioral-usage analytics, or third-party tracking. No GeneFox account is required. Bookmarks stay private and are portable via export/import. DATA SOURCES Consult each provider's site for the authoritative source: • NCI Genomic Data Commons (TCGA and related programs): https://gdc.cancer.gov • NCBI Gene Expression Omnibus (GEO): https://www.ncbi.nlm.nih.gov/geo/ • ARCHS4 fallback terms and citation: https://archs4.org/help • GTEx Portal: https://gtexportal.org • UCSC Xena: https://xenabrowser.net • Treehouse Cell Line Compendium v1 (CCLE, July 2019): https://treehousegenomics.ucsc.edu/public-data-html/previous-compendia/ • Treehouse Tumor Compendium 25.01: https://treehousegenomics.ucsc.edu/public-data/ DISCLAIMER GeneFox is an independent, nonclinical app for scientific research. It is NOT a government app and is not affiliated with or endorsed by any government entity or agency (including the U.S. NIH, NCI, or NCBI) or any data provider above. GeneFox is not a medical device and does not diagnose, treat, cure, or prevent any medical condition. Consult a qualified healthcare professional for medical advice, diagnosis, or treatment. Its outputs are not validated for clinical decision-making. GeneFox is developed by Vindhya Data Science.

  • 5.0
    out of 5
    2 Ratings

• GeneFox no longer quits without warning on Mac. A background task inside the cloud-sync library could fail writing to its own cache and take the whole app down, with no chance for GeneFox to intervene. That cache is gone; nothing depended on it. • A saved report that refused to reopen now opens. A report holding a figure captured at a high colour depth — usually a heatmap — saved correctly, then called itself corrupt on every later load. It was neither corrupt nor too large. Reports already stuck this way open now. • A pan-cancer figure exports whole instead of being quietly cropped. Exporting all 54 cohorts at a single-column width cut off the lower cohorts and baked the provenance text into the image, without saying so. • A project list no longer empties because one project came from a newer version. A single unreadable project stopped the whole list loading. It is now skipped and the rest open. Saved analysis recipes had the same flaw and the same fix. • A saved view you opened once no longer reopens itself days later. Some corrections change figures or numbers you may already have exported. If you relied on any of these, it is worth regenerating the figure: • Compare Cohorts no longer reports a p-value across arms that share patients. With adjacent normal included, a cohort contributes both its tumour arm and its own adjacent-normal arm — the same people. Those groups are not independent, and a p-value obtained that way is not one to report. • Box plots no longer drop their most extreme outliers. A box drew at most 100 outliers and took the first 100 of an ascending list, so a box with many low outliers showed none of its high ones, and the axis shrank to match. • A heatmap gene row containing an infinity now scales correctly. Such a row was drawn flat and mid-toned across every sample — the same picture as a gene that genuinely does not vary — rather than as a visible gap. • The gene-correlates figure's threshold lines now sit where its caption says they do. • Small p-values are printed the same way everywhere. No p-value changed; only how a small one is displayed.

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Seller
Vindhya Data Science Inc.
Size
55.5 MB
Category
Reference
Compatibility
Requires iOS 17.6 or later.
  • iPhone
    Requires iOS 17.6 or later.
  • iPad
    Requires iPadOS 17.6 or later.
  • Mac
    Requires macOS 14.0 or later.
  • Apple Vision
    Requires visionOS 1.3 or later.
Languages
English
Age Rating
13+
  • 13+
  • Infrequent
    Alcohol, Tobacco, Drug Use or References
Copyright
© Vindhya Data Science