# How to cite PEPkit

Thanks for citing us! If you use the PEP tools, or concepts in your research, please cite us!

| If you use... | Please cite ... |
|---------------|-----------------|
| PEP specification | Sheffield et al. (2021) *GigaScience* |
| `eido` | Sheffield et al. (2021) *GigaScience* |
| `geofetch` | Sheffield et al. (2021) *GigaScience*; Khoroshevskyi et al. (2023) |
| `looper` | Sheffield et al. (2021) *GigaScience* |
| `PEPhub` | Sheffield et al. (2021) *GigaScience*; LeRoy et al. (2024) *GigaScience* |
| `peppy` | Sheffield et al. (2021) *GigaScience* |
| `pypiper` | Sheffield et al. (2021) *GigaScience* |
| `pipestat` | Sheffield et al. (2021) *GigaScience* |


## Full citation information

<span class="authors">Sheffield NC, Stolarczyk M, Reuter VP, and Rendeiro A.</span><br/>
<span class="paper-title">Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects</span>
<br /><i>GigaScience</i> (2021)
<span class="doi">DOI: <a href="http://dx.doi.org/10.1093/gigascience/giab077">10.1093/gigascience/giab077</a></span>


<span class="authors">O Khoroshevskyi, N LeRoy, VP Reuter, NC Sheffield.</span><br/>
<span class="paper-title">GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA</span>
<br /><i>Bioinformatics 39 (3), btad069</i> (2023)
<span class="doi">DOI: <a href="http://dx.doi.org/10.1093/bioinformatics/btad069">10.1093/bioinformatics/btad069</a></span>


<span class="authors">NJ LeRoy, O Khoroshevskyi, A O’Brien, R Stepień, A Arslan, NC Sheffield.</span><br/>
<span class="paper-title">PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata</span>
<br /><i>GigaScience</i> (2024)
<span class="doi">DOI: <a href="http://dx.doi.org/10.1093/gigascience/giae033">10.1093/gigascience/giae033</a></span>