Frequently asked questions

RNA-seq gene expression for the 33 TCGA cancer cohorts, from the NCI Genomic Data Commons, with sample and clinical information such as sample type, age, gender, race and overall survival. The single-cell workflow has its own datasets, and you can build more from your own files. There is no miRNA, DNA methylation or mutation data.

TCGA is a finished project, and Blueprint serves a fixed snapshot of it; it does not follow new GDC releases automatically. The Downloads page shows the Blueprint catalogue release you are browsing, such as tcga-v1.

Raw counts, variance-stabilised values, TPM and FPKM, depending on the analysis. Differential expression with DESeq2, edgeR or limma-voom always uses raw counts, and survival analysis uses TPM.

Yes: tables in the plot builder, PCA and differential expression, and single-cell data through the dataset builder. Sign in before you upload. Use your own data gives the formats and size limits.

Four workflows: differential expression with DESeq2, edgeR, limma-voom or limma; PCA and its variants; a survival signature built from a Cox screen, a LASSO-Cox signature and an evaluation; and single-cell RNA-seq on Scanpy or Seurat. The Visualization tab on Analysis adds the plot types.

It depends on the data. By default one figure render stops after 30 seconds, in the plot builder and on the analysis pages alike, and an analysis after 10 minutes (45 for dynamical RNA velocity). You can have 20 unfinished jobs of each kind at once.

You ran it before with the same settings, so your stored result came back. Use Clear Cache Data on the analysis page to run it again from scratch.

Charts on the analysis pages (PCA, differential expression, survival and single-cell) show the values of the point under the pointer: a sample on the PCA scatter, a gene on the volcano plot, a cell on single-cell maps. Figures from the plot builder are images: zoom them from 50% to 200% or open them full screen.

Figures come as SVG, PNG, PDF, JPEG or TIFF, depending on the plot; catalogue plots take a DPI from 50 to 600 for raster output. Tables come as TSV, CSV or TXT for differential results, and CSV, TSV or Parquet for PCA exports. TCGA files are tab-separated.

Yes. SVG is always vector, and figures drawn on the server (the plot builder, catalogue plots and the static figure cards on the analysis pages) also give vector PDFs and raster files up to 600 DPI. The PCA page's variance, loadings, contribution and distribution charts are exported from the browser at twice screen resolution, and even their PDF is a bitmap, so use SVG for those. Check your journal's figure requirements before you submit, and cite the data.

Not to browse projects, the analysis gallery, the download catalogue or the developer documentation. You need one to make figures, run analyses, see per-sample tables, download TCGA files, keep a history and use your uploads.

Today, nothing you can use: every feature works on a free account, under the same limits for everyone. The Upgrade page lists the Pro and Max plans; its comparison table describes the plans, not limits enforced today.

Passwords are stored as bcrypt hashes and sign-in tokens as SHA-256 hashes. Your access token lives only in the browser's memory and expires after 15 minutes by default. In Settings → Account you can add two-factor authentication and see or sign out every device. The Privacy Policy explains what is collected and why.

In Settings → Privacy. Export data downloads a ZIP of your account records as JSON (profile, settings, upload records, sessions, orders and data requests), available for 7 days; it does not include your files, figures or results. Request data erasure permanently deletes your uploads, figures, analyses and history and closes the account, within 30 days. Delete account in Settings → Account does it at once. (The Export your data card beside it is not live yet; use the export under Privacy.)

History lists your figures and analysis runs only while Keep analysis history is on in Settings → Privacy. Nothing is recorded while it is off, and turning it off also hides what was recorded before.

Acknowledge TCGA with the wording NCI asks for, shown below, and cite the Genomic Data Commons: Heath AP et al., The NCI Genomic Data Commons, Nat Genet 53, 257–262 (2021). Cite the methods you ran, such as DESeq2, limma or Seurat, as their authors ask.