Built with open-source software, original site content and respect for study authors.
Examples and original content
Public biological datasets are not hosted. RNA examples and toolkit demonstration values are synthetic or explicitly hypothetical. Educational diagrams and guides are original. User-uploaded files remain on the user’s device.
Metabolic network reference (Tool 17)
The scRNA–Metabolomics Integrator uses reduced versions of Human-GEM 2.1.1 and Mouse-GEM 1.8.0 by SysBioChalmers and contributors, licensed under CC BY 4.0. Changes: reduced to metabolite identifiers, gene–reaction rules, reaction direction and subsystem; exchange, biomass and artificial reactions removed. See the notice and change log and the license text. Please cite Robinson et al., Sci Signal 2020;13:eaaz1482 and Wang et al., PNAS 2021;118:e2102344118. These are curated knowledge resources, not experimental study datasets.
RNA Atlas browser components
- Graphology 0.26.0 / Louvain 2.0.2 — MIT. Graphology license; Louvain license. All bundled graph component versions and licenses; individual license files are retained alongside the bundle.
- UMAP-JS 1.4.0 — Apache-2.0. Bundled license.
- h5wasm 0.10.3 — MIT. Bundled license; HDF5 component notices remain with the runtime.
- pako 2.1.0 — MIT/Zlib. Bundled license; streaming checked gzip decoding.
- Optional sample-pathway engine: GSVA 2.4.9 (Artistic-2.0), including ssGSEA; edgeR/limma provide the explicitly described preprocessing and score models. Packages are installed locally; exact versions and their original notices are retained in that environment.
- Optional local companion: SoupX 1.6.2 and CellTypist 1.7.1. Original license/source notices apply to packages installed locally; no pretrained public model or experimental dataset is bundled.
- webR 0.6.0 — GPL-3.0 with R and component licenses. Bundled notice.
- Pyodide 314.0.7 — MPL-2.0 with CPython and component licenses. MPL notice.
- hash-wasm 4.12.0 — MIT. Bundled license.
- Browser limma 3.99.2 and statmod 1.5.2 — GPL terms as recorded in their package notice and hash manifest; GPL-2 and GPL-3 texts are retained.
Upstream source links provide corresponding source and full component license information. The optional local Python companion uses Scrublet, harmonypy, leidenalg, igraph, scikit-learn, Scanpy and AnnData, with NumPy/SciPy and their dependencies. These packages are installed on the user’s computer rather than bundled into the website. Native-engine packages retain their original licenses in the user-built environment; its download includes software and method notes. No package or author endorses this project.
Hub design and content
The hub uses original HTML, CSS, JavaScript and SVG artwork with system fonts. New shared-shell code is provided under the MIT license. Original hub and toolkit prose, interview questions, glossary entries and illustrations may be reused with attribution to SolveEverything under CC BY 4.0. These permissions do not relicense third-party software, datasets or earlier RNA analysis sources.
Interactive toolkit charts use locally bundled Chart.js 4.5.1 (MIT). Toolbar icons use Lucide 0.468.0 (ISC, with retained Feather attribution). Sources: Chart.js and Lucide. No paid fonts, images, analytics or APIs are used.
Corrections
For missing attribution or a reuse concern, see Contact & corrections. Source-repository and owner contact links await configuration.
Gene annotations
Gene data from Ensembl. Tool 15 retrieves user-requested transcript, exon, sequence and protein-feature annotations from the free Ensembl REST API. Assembly, stable IDs/versions and fetch time are retained with the reference. Projected domain consequences are local predictions, not Ensembl variant annotations.