Citing

Citing benchsiDE and its data sources

The application

Cite benchsiDE with the version you used (shown in the header and in the methods text). Citation metadata is in CITATION.cff in the repository; GitHub displays it under Cite this repository.

Methods and resources

The auto-generated methods text includes the citation for every method and resource used in your analysis. Copy it from the application rather than from this page, because it reflects your settings.

Resource	Citation
edgeR (TMM, filterByExpr)	Robinson MD and Oshlack A (2010) Genome Biol 11:R25; Chen Y, Lun ATL and Smyth GK (2016) F1000Research 5:1438
limma (moderated t, F)	Smyth GK (2004) Stat Appl Genet Mol Biol 3:Article3; Ritchie ME et al. (2015) Nucleic Acids Res 43:e47
voom	Law CW et al. (2014) Genome Biol 15:R29
CAMERA	Wu D and Smyth GK (2012) Nucleic Acids Res 40:e133
FRY / ROAST	Wu D et al. (2010) Bioinformatics 26:2176
GSEA	Subramanian A et al. (2005) PNAS 102:15545
RRHO	Plaisier SB et al. (2010) Nucleic Acids Res 38:e169
MSigDB Hallmark	Liberzon A et al. (2015) Cell Syst 1:417
Mouse MSigDB	Castanza AS et al. (2023) Nat Methods 20:1619
Gene Ontology	Ashburner M et al. (2000) Nat Genet 25:25; Gene Ontology Consortium (2023) Genetics 224:iyad031
Reactome	Milacic M et al. (2024) Nucleic Acids Res 52:D672
HGNC	Seal RL et al. (2023) Nucleic Acids Res 51:D1003
MGI	Baldarelli RM et al. (2024) Genetics 227:iyae031
Silhouette	Rousseeuw PJ (1987) J Comput Appl Math 20:53
WGCNA connectivity	Zhang B and Horvath S (2005) Stat Appl Genet Mol Biol 4:Article17

Licenses of embedded data

Resource	License
MSigDB gene sets	CC BY 4.0
MGI annotation and homology data	CC BY 4.0
RGD annotation data	CC BY 4.0
HGNC data	CC0 1.0
Plotly.js	MIT

The embedded MGI, RGD and HGNC data are subsets of the source files (selected columns, re-encoded). The licenses link in the application header shows the full notice; see also THIRD_PARTY_NOTICES.md.