PEP in practice

Software using PEP

Publicly available software that builds on PEP:

Demo data using PEP

Real datasets organized in PEP format:

Publications that use PEP software:

Sheffield et al. 2020. Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects. BioRxiv.

Zhou et al. 2020. CATA: a comprehensive chromatin accessibility database for cancer BioRxiv.

Weber et al. 2020. Transient “rest” induces functional reinvigoration and epigenetic remodeling in exhausted CAR-T cells. BioRxiv.

Granja et al. 2020. ArchR: An integrative and scalable software package for single-cell chromatin accessibility analysis BioRxiv.

Smith et al. 2020. Quality control and processing of nascent RNA profiling data BioRxiv.

Ram-Mohan et al. 2020. Integrative profiling of early host chromatin accessibility responses in human neutrophils with sensitive pathogen detection BioRxiv.

Fan et al. 2020. Epigenetic reprogramming towards mesenchymal-epithelial transition in ovarian cancer-associated mesenchymal stem cells drives metastasis BioRxiv.

Stolarczyk et al. 2020. Refgenie: a reference genome resource manager GigaScience.

Corces et al. 2018. The chromatin accessibility landscape of primary human cancers. Science.

Datlinger et al. 2017. Pooled CRISPR screening with single-cell transcriptome readout Nature Methods.

Sheffield et al. 2017. DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma Nature Medicine.

PEP shield

If your project is PEP-compatible, please add it to this list with a pull request and use this shield to showcase PEP:

PEP compatible

Here's markdown (for use on GitHub READMEs):

[![PEP compatible](](


<a href=""><img src="" alt="PEP compatible" style="float:left; margin:10px"></a>