How to cite datasets and HypoExplorer

Credit the original publication, the deposited dataset and HypoExplorer separately. Describe the comparison you used so another researcher can find the same data and understand your analysis.

Wenyuan He created HypoExplorer and holds a PhD from the University of Toronto. About the author.

What to cite

Original publication. Cite the source article using its authors, title and DOI or PMID. The study overview pages link to verified publication records where available. Retrieve the final journal formatting from the publisher or PubMed.
Deposited dataset. Include the repository name and accession, such as a GEO series number, plus its source-record link. If a deposit has no linked paper, cite the deposit without inventing a publication.
Interface and selected analysis. Credit Wenyuan He as the author of HypoExplorer. Include the study overview URL and your access date. State the comparison, track or population, relevant settings and any exported data or figure you used.

The About page has the app author's biography and contact details.

Suggested interface reference

He, Wenyuan. HypoExplorer [web application; beta]. https://hypoexplorer.com. Accessed [your actual access date].

Replace the access-date placeholder with the date you used the app. Download the software citation file and save the release metadata with your results. Record the app version, full release identifier, source fingerprint and data build identifiers supplied in your export. The source fingerprint identifies working-tree builds too. This reference cites the website, not a peer-reviewed software paper. Do not assign an original study's DOI to HypoExplorer.

The source repository contains the release packaging command and checksums. A public archive DOI has not yet been assigned; until an immutable archive is deposited, retain the exported result files and release metadata.

Source citation examples

GSE236077: Mouse hypothalamus — chow vs HFD (brain atlas; bulk RNA-seq)

Source publication: Todorov PV et al. An RNA-seq atlas of mouse brain areas during fasting and diet-induced obesity. DOI 10.1038/s41597-023-02888-4.

Dataset deposit: GSE236077 original repository record.

The HypoExplorer study overview describes the HFD versus Chow comparison. Record the track or population and any additional comparison you used.

This is the selected hypothalamus comparison from a wider brain atlas. Cite the original atlas, and state the selected region and comparison rather than implying you analysed every deposited sample.

CNP0003785: Macaque hypothalamus (snRNA-seq)

Source publication: Lei Y et al. Region-specific transcriptomic responses to obesity and diabetes in macaque hypothalamus. DOI 10.1016/j.cmet.2024.01.003.

Dataset deposit: CNP0003785 original repository record.

The HypoExplorer study overview describes the Obese versus Normal comparison. Record the track or population and any additional comparison you used.

The macaque example is an obese-versus-normal reanalysis of the Lei et al. source cohort. The source article is not a publication of this reanalysis, and the reanalysis does not currently have its own publication citation.

What to record in your methods or figure caption

The source accession, publication and selected species, tissue and assay.
The case and baseline groups, track or population, exclusions, and biological replicate counts.
The expression unit, differential-expression method and any display or significance thresholds relevant to the claim.
For pathways, the gene-set collection, pathway identifier, direction, NES and adjusted p-value, plus the methods and source data used.
The stable study overview URL, access date, and the exported data or figure used.

Use the Methods and data interpretation guide to distinguish a published author result, a local reanalysis and a new exploratory comparison. A figure made with the interface does not establish that the original authors tested the same hypothesis.

Reuse and corrections

HypoExplorer's original code is licensed under MIT. Its original contributions to derived analysis outputs are licensed under CC BY 4.0. See the scope and attribution statement. Original publications, deposited data, gene-set collections, annotations, fonts and dependencies retain their own terms; the HypoExplorer licenses do not replace them.

HypoExplorer is in beta testing. Save the results and settings you used because the interface, analyses and coverage may change. For citation corrections, contact wenyuan.he@mail.utoronto.ca and include the affected study accession and publication link.