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PEPkit usage statistics

This page documents usage of PEPkit-related tools:

  1. statistics of downloads of packages from PyPI
  2. other software packages that use PEPkit software
  3. datasets organized in PEP-compatible formats
  4. publications that reference PEP manuscripts

PyPI download history

Software using PEPkit

Publicly available software that builds on PEP:

Demo data using PEPkit

Real datasets organized in PEP format:

Publications that use PEPkit:

  • Nash et al. (2023). Maternal diet alters long-term innate immune cell memory in fetal and juvenile hematopoietic stem and progenitor cells in nonhuman primate offspring
    Cell Reports. DOI: 10.1016/j.celrep.2023.112393
  • Danko et al. (2023). Evolution of promoter-proximal pausing enabled a new layer of transcription control
    DOI: 10.21203/
  • Singh et al. (2023). Cohesin regulates alternative splicing
    Science Advances. DOI: 10.1126/sciadv.ade3876
  • Luo et al. (2023). Epiblast-like stem cells established by Wnt/-catenin signaling manifest distinct features of formative pluripotency and germline competence
    Cell Reports. DOI: 10.1016/j.celrep.2023.112021
  • Abadie et al. (2022). Flexible and scalable control of T cell memory by a reversible epigenetic switch
    DOI: 10.1101/2022.12.31.521782
  • Wolpe et al. (2022). Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling
    DOI: 10.1101/2022.12.08.519600
  • Robbe et al. (2022). Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features
    Nature Genetics. DOI: 10.1038/s41588-022-01211-y
  • Robey et al. (2022). The methyltransferases METTL7A and METTL7B confer resistance to thiol-based histone deacetylase inhibitors
    DOI: 10.1101/2022.10.07.511310
  • Callahan et al. (2022). High enhancer activity is an epigenetic feature of HPV negative atypical head and neck squamous cell carcinoma
    Frontiers in Cell and Developmental Biology. DOI: 10.3389/fcell.2022.936168
  • Duvall et al. (2022). Single-cell transcriptome and accessible chromatin dynamics during endocrine pancreas development
    Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.2201267119
  • Taklifi et al. (2022). Integrating chromatin accessibility states in the design of targeted sequencing panels for liquid biopsy
    Scientific Reports. DOI: 10.1038/s41598-022-14675-z
  • Grandi et al. (2022). Chromatin accessibility profiling by ATAC-seq
    Nature Protocols. DOI: 10.1038/s41596-022-00692-9
  • Hunter et al. (2022). HNF4A modulates glucocorticoid action in the liver
    Cell Reports. DOI: 10.1016/j.celrep.2022.110697
  • O'Connor et al. (2022). BET Protein Inhibition Regulates Macrophage Chromatin Accessibility and Microbiota-Dependent Colitis
    Frontiers in Immunology. DOI: 10.3389/fimmu.2022.856966
  • Wang et al. (2022). Prediction of histone post-translational modification patterns based on nascent transcription data
    Nature Genetics. DOI: 10.1038/s41588-022-01026-x
  • Zhang et al. (2022). Extensive evaluation of ATAC-seq protocols for native or formaldehyde-fixed nuclei
    BMC Genomics. DOI: 10.1186/s12864-021-08266-x
  • Shahin et al. (2021). Germline biallelic mutation affecting the transcription factor Helios causes pleiotropic defects of immunity
    Science Immunology. DOI: 10.1126/sciimmunol.abe3981
  • Ram-Mohan et al. (2021). Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detection
    Life Science Alliance. DOI: 10.26508/lsa.202000976
  • Robertson et al. (2021). Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes
    Nature Genetics. DOI: 10.1038/s41588-021-00880-5
  • Cheung et al. (2021). Repression of CTSG, ELANE and PRTN3-mediated histone H3 proteolytic cleavage promotes monocyte-to-macrophage differentiation
    DOI: 10.1038/s41590-021-00928-y
  • Hasegawa et al. (2021). Clonal inactivation of telomerase promotes accelerated stem cell differentiation
    bioRxiv. DOI: 10.1101/2021.04.28.441728
  • Weber et al. (2021). Transient rest restores functionality in exhausted CAR-T cells through epigenetic remodeling
    Science. DOI: 10.1126/science.aba1786
  • Gharavi et al. (2021). Embeddings of genomic region sets capture rich biological associations in low dimensions
    Bioinformatics. DOI: 10.1093/bioinformatics/btab439
  • Tovar et al. (2021). Integrative phenotypic and genomic analyses reveal strain-dependent responses to acute ozone exposure and their associations with airway macrophage transcriptional activity
    bioRxiv. DOI: 10.1101/2021.01.29.428733
  • Granja et al. (2021). ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis
    Nature Genetics. DOI: 10.1038/s41588-021-00790-6
  • Gu et al. (2021). Bedshift: perturbation of genomic interval sets
    Genome Biology. DOI: 10.1186/s13059-021-02440-w
  • Mölder et al. (2021). Sustainable data analysis with Snakemake
    F1000Research. DOI: 10.12688/f1000research.29032.2
  • Smith et al. (2021). PEPPRO: quality control and processing of nascent RNA profiling data
    Genome Biology. DOI: 10.1186/s13059-021-02349-4
  • Fan et al. (2020). Epigenomic Reprogramming toward Mesenchymal-Epithelial Transition in Ovarian-Cancer-Associated Mesenchymal Stem Cells Drives Metastasis
    Cell Reports. DOI: 10.1016/j.celrep.2020.108473
  • ROBERTSON et al. (2020). 112-OR: Integrative Analysis of Chromatin Accessibility and Genetic Risk in T1D Patients and Controls
    Diabetes. DOI: 10.2337/db20-112-or
  • Smith and Sheffield (2020). Analytical Approaches for ATAC-seq Data Analysis
    Current Protocols in Human Genetics. DOI: 10.1002/cphg.101
  • Liu (2020). Clinical implications of chromatin accessibility in human cancers
    DOI: 10.18632/oncotarget.27584
  • Zhou et al. (2020). CATA: a comprehensive chromatin accessibility database for cancer
    bioRxiv. DOI: 10.1101/2020.05.16.099325
  • Wang et al. (2020). Interdependence between histone marks and steps in Pol II transcription
    DOI: 10.1101/2020.04.08.032730
  • Cai et al. (2020). Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain
    DOI: 10.1186/s12920-020-0695-0
  • Li et al. (2020). Acetate supplementation restores chromatin accessibility and promotes tumor cell differentiation under hypoxia
    Cell Death &$$ Disease. DOI: 10.1038/s41419-020-2303-9
  • Stolarczyk et al. (2020). Refgenie: a reference genome resource manager
    GigaScience. DOI: 10.1093/gigascience/giz149
  • Liang et al. (2019). Global changes in chromatin accessibility and transcription following ATRX inactivation in human cancer cells
    DOI: 10.1002/1873-3468.13549
  • Corces et al. (2018). The chromatin accessibility landscape of primary human cancers
    Science. DOI: 10.1126/science.aav1898
  • Datlinger et al. (2017). Pooled CRISPR screening with single-cell transcriptome readout
    Nat. Methods. DOI: 10.1038/nmeth.4177
  • Sheffield et al. (2017). DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma
    Nature Medicine. DOI: 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:

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>