PEP in practice
Software using PEP
Publicly available software that builds on PEP:
- PEPATAC - An ATAC-seq pipeline.
- PEPPRO - An nascent RNA profiling pipeline (PRO-seq, GRO-seq, ChRO-seq).
- peppy
- pepr
- geofetch - Converts GEO or SRA accessions into PEP projects.
- divcfg
- pifaces
- pypiper
- dnameth_pipelines
- projectInit
- ngstoolkit - NGS analysis toolkit
- BiocProject
Demo data using PEP
- example_peps repository - A collection of example PEPs demonstrating various features.
- microtest
- hello looper! example
Real datasets organized in PEP format:
- https://github.com/epigen/crop-seq
- https://github.com/epigen/baf_complex
- https://github.com/epigen/mthfd1
- https://github.com/epigen/cll-ibrutinib_time
- https://github.com/epigen/cll-ibrutinib
- https://github.com/epigen/cll-chromatin
Publications that use PEP software:
Sheffield et al. 2020. Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects. BioRxiv. https://doi.org/10.1101/2020.10.08.331322
Zhou et al. 2020. CATA: a comprehensive chromatin accessibility database for cancer BioRxiv. https://doi.org/10.1101/2020.05.16.099325
Weber et al. 2020. Transient “rest” induces functional reinvigoration and epigenetic remodeling in exhausted CAR-T cells. BioRxiv. https://doi.org/10.1101/2020.01.26.920496
Granja et al. 2020. ArchR: An integrative and scalable software package for single-cell chromatin accessibility analysis BioRxiv. https://doi.org/10.1101/2020.04.28.066498
Smith et al. 2020. Quality control and processing of nascent RNA profiling data BioRxiv. https://doi.org/10.1101/2020.02.27.956110
Ram-Mohan et al. 2020. Integrative profiling of early host chromatin accessibility responses in human neutrophils with sensitive pathogen detection BioRxiv. https://doi.org/10.1101/2020.04.28.066829
Fan et al. 2020. Epigenetic reprogramming towards mesenchymal-epithelial transition in ovarian cancer-associated mesenchymal stem cells drives metastasis BioRxiv. https://doi.org/10.1101/2020.02.25.964197
Stolarczyk et al. 2020. Refgenie: a reference genome resource manager GigaScience. https://doi.org/10.1093/gigascience/giz149
Corces et al. 2018. The chromatin accessibility landscape of primary human cancers. Science. https://doi.org/10.1126/science.aav1898
Datlinger et al. 2017. Pooled CRISPR screening with single-cell transcriptome readout Nature Methods. https://doi.org/10.1038/nmeth.4177
Sheffield et al. 2017. DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma Nature Medicine. https://doi.org/10.1038/nm.4273
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:
Here's markdown (for use on GitHub READMEs):
[](http://pepkit.github.io)
Or HTML:
<a href="http://pepkit.github.io"><img src="http://pepkit.github.io/img/PEP-compatible-green.svg" alt="PEP compatible" style="float:left; margin:10px"></a>