How to cite PEPkit

Thanks for citing us! If you use the PEP tools, or concepts in your research, here are papers you can cite.

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. (2023) bioRxiv
peppy	Sheffield et al. (2021) GigaScience
pypiper	Sheffield et al. (2021) GigaScience
pipestat	Sheffield et al. (2021) GigaScience

Full citation information

Sheffield NC, Stolarczyk M, Reuter VP, and Rendeiro A.
Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects
GigaScience (2021) DOI: 10.1093/gigascience/giab077

O Khoroshevskyi, N LeRoy, VP Reuter, NC Sheffield.
GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA
Bioinformatics 39 (3), btad069 (2023) DOI: 10.1093/bioinformatics/btad069

NJ LeRoy, O Khoroshevskyi, A O’Brien, R Stepień, A Arslan, NC Sheffield.
PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata
bioRxiv (2023) DOI: 10.1101/2023.08.15.551388