Before sharing lisaR, a resource or a report, identify which material you are sharing. The software licence, fixed LISA annotations, third-party scientific resources and your own study material have different notices and conditions. One licence does not replace the others.
Where a report presents category-level adjusted P and minimum supported d/N, its methods use robust Hommel closed testing. Cite Goeman et al. (2019), Biometrika 106, 841–856, doi:10.1093/biomet/asz041, alongside the study’s data and gene-set resource sources. This method attribution does not replace provider licences or justify biological claims beyond the saved analysis.
| Material | Where its conditions come from | What to keep with it |
|---|---|---|
| lisaR code, documentation and synthetic fixtures | DESCRIPTION and inst/COPYING |
Package name and version, GPL-3.0-or-later notice, copyright holder, author and corresponding source obligations when distributing covered copies. |
| Fixed LISA dictionaries and category map in this candidate | Installed resource manifest, provenance and third-party notices | Exact resource IDs, SHA-256 records, LISA/CSIC notice and applicable MSigDB, KEGG or BioCarta attribution. |
| External TERM2GENE memberships and native pathway material | The provider’s current terms and the recipient’s authorised acquisition route | Provider attribution, exact release or snapshot identity and any collection-specific notices. |
| R package dependencies | Each dependency’s own licence | The notices and sources required for the form in which you distribute them. |
| Your input data and generated report | Your data source, consent/governance, study agreements and incorporated resources | Study citations, data provenance, resource inventory and any provider notices that apply to included material. |
This guide reports the notices installed with lisaR. It does not create a new permission or settle whether a particular dataset or report may be distributed.
lisaR includes the exact lisa_dictionary_core@1.0.0,
lisa_dictionary_expanded@1.0.0 and
lisa_category_map@1.0.0 resources. They record fixed
gene-set-to-category assignments and category organisation, not external
gene memberships.
The installed provenance records the CSIC/LISA annotations and
retains MSigDB, KEGG and BioCarta attribution where their identifiers
occur. The resource manifest identifies the bundled annotations and
their source-specific conditions. Do not treat
GPL-3.0-or-later as permission to redistribute third-party
memberships or diagrams.
The installed third-party notice records that MSigDB identifies KEGG MEDICUS content as CC BY-SA 4.0 and describes one-way compatibility from CC BY-SA 4.0 to GPLv3 for adapted material. That compatibility does not remove MSigDB or KEGG attribution and does not replace collection-specific conditions.
The current technical reconstruction is tied to MSigDB 2026.1 through
msigdbr 26.1.0. The original historical model-assisted
annotation retrieval release is unrecorded. These are separate
provenance facts. See How LISA
dictionaries were built for the source-backed history and its
limits.
| External material | Installed notice |
|---|---|
| MSigDB identifiers or TERM2GENE memberships | Retain Molecular Signatures Database attribution and the applicable collection-specific conditions. Review the MSigDB licence terms. |
| KEGG MEDICUS or KEGG LEGACY identifiers, KGML or pathway images | Retain MSigDB and KEGG attribution where applicable and review the KEGG copyright and licence information. A user-authorised cache snapshot is not part of the lisaR software licence. |
| BioCarta identifiers or memberships | Retain MSigDB and BioCarta acknowledgement and disclaimer conditions linked from the MSigDB terms. |
The MSigDB preparation helper asks a recipient to assert acceptance only before the supported public acquisition. That assertion permits the call; it does not grant a licence, accept terms for another person or confer redistribution rights. A recorded resource ID or SHA-256 likewise proves identity, not permission.
Dependencies retain their own licences. If you redistribute an installed library, container or other combined form, review the actual dependency set and the notices required for that distribution. Installing a dependency does not replace the terms for scientific content retrieved through it.
Inspect the citation generated from the exact installed package metadata:
Cite the version used in your analysis. For this beta, R derives the software citation from the installed package metadata.
Cite the study data and analytical methods used in your work. For external gene-set resources, follow the provider’s current citation instructions and record the exact release used. The installed resource provenance names Molecular Signatures Database, Liberzon et al. and Subramanian et al.; consult the provider material for the complete citations appropriate to your selected release and collections.
Use the installed paths rather than copying notices from another lisaR version:
system.file("COPYING", package = "lisaR")
system.file("THIRD_PARTY_NOTICES.md", package = "lisaR")
system.file(
"extdata", "dictionaries", "RESOURCE_PROVENANCE.tsv",
package = "lisaR"
)Read those files before redistribution. If the status or terms of material you intend to share remain ambiguous, keep that material private until the relevant rights holder or institutional process resolves the question.