bioCancer is licensed under AGPL3 (http://www.tldrlegal.com/l/AGPL3). The bioCancer help files are licensed under the creative commons attribution, non-commercial, share-alike license CC-NC-SA (http://creativecommons.org/licenses/by-nc-sa/4.0/).

As a summary, the AGPLv3 license requires, attribution, including copyright and license information in copies of the software, stating changes if the code is modified, and disclosure of all source code. Details are in the COPYING file.


bioCancer uses resources from multiple packages and databases:

-1 for gene/study Classifier [1]
-2 for gene set Clustering [2]
-3 Disease Ontology [3]
-4 for Network and Pathway enrichment : Reactome [4,5]
-5 for Disease Gene Association: DisGeNET [6,7,8]
-6 Processing panel is implemented from radiant package develpped by Dr Vincent Nijs available at https://github.com/vnijs/radiant

References

1- Aibar S, Fontanillo C, Droste C, Roson-Burgo B, Campos-Laborie F, Hernandez-Rivas J and De Las Rivas J (2015). “Analyse multiple disease subtypes and build associated gene networks using genome-wide expression profiles.” BMC Genomics, 16(Suppl 5). http://doi.org/10.1186/1471-2164-16-S5-S3.

2- Yu G, Wang L, Han Y and He Q (2012). “clusterProfiler: an R package for comparing biological themes among gene clusters.” OMICS: A Journal of Integrative Biology, 16(5), pp. 284-287. http://doi.org/10.1089/omi.2011.0118

3- G Yu, LG Wang, GR Yan, QY He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609.

4- Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, D'Eustachio P, Stein L. Annotating cancer variants and anti-cancer therapeutics in reactome. Cancers (Basel). 2012 Nov 8;4(4):1180-211. doi: 10.3390/cancers4041180.

5- Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P. The Reactome pathway knowledgebase. Nucleic Acids Res. 2014 Jan;42(Database issue):D472-7. doi: 10.1093/nar/gkt1102. Epub 2013 Nov 15.

6- Janet Piñero, Núria Queralt-Rosinach, Àlex Bravo, Jordi Deu-Pons, Anna Bauer-Mehren, Martin Baron, Ferran Sanz, Laura I Furlong. DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. Database (2015) Vol. 2015: article ID bav028; doi:10.1093/database/bav028

7- Anna Bauer-Mehren, Markus Bundschus, Michael Rautschka, Miguel A. Mayer, Ferran Sanz, Laura I. Furlong. Gene-disease network analysis reveals functional modules in mendelian, complex and environmental diseases. PLoS ONE 2011 6(6): e20284. doi:10.1371/journal.pone.0020284.

8- Bauer-Mehren A, Rautschka M, Sanz F, Furlong LI. DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks. Bioinformatics. 2010 Nov 15;26(22):2924-6. Epub 2010 Sep 21
