PEPkit usage statistics

This page documents usage of PEPkit-related tools:

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

Download history

Monthly downloads of PEPkit packages. Data is harvested from PyPI and CRAN by databio/stats and refreshed on the first of each month.

PyPI

CRAN

Software using PEPkit

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 PEPkit

• 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 PEPkit:

78 publications. This list is updated monthly by an automated search; see publications.yaml for the machine-readable source.

• Botts et al. (2026). ERG preserves endothelial identity to limit atherosclerosis
  Nature Communications. DOI: 10.1038/s41467-026-75287-z
• Brown et al. (2026). Using semantic search to find publicly available gene-expression datasets
  Bioinformatics. DOI: 10.1093/bioinformatics/btag053
• Du et al. (2026). SCSEQ: A web tool for analyzing single-cell RNA-seq data
  GigaScience. DOI: 10.1093/gigascience/giag029
• Hossain et al. (2026). ChromAcS: an automated and flexible GUI for end-to-end reproducible ATAC-seq analysis across multiple species
  BMC Bioinformatics. DOI: 10.1186/s12859-026-06382-7
• Ma et al. (2026). Chromatin accessibility directly governs flavonoid biosynthesis and indirectly orchestrates cannabinoid production in Cannabis
  Frontiers in Plant Science. DOI: 10.3389/fpls.2025.1687700
• Medina-Ortiz et al. (2026). Perspectives Chapter: Data-Centric Strategies for Machine Learning-Driven Therapeutic Peptide Design – Challenges and Perspectives
  Data Quality Matters - Best Practices for Integrity and Assurance. DOI: 10.5772/intechopen.1013230
• Mueller et al. (2026). ppGpp regulates transcription elongation via direct and indirect inputs to RNA polymerase pausing and nucleotide addition
  DOI: 10.64898/2026.05.13.724835
• Mukherjee and Guertin (2026). Genome-wide dynamic nascent transcript profiles reveal that most paused RNA polymerases terminate
  Nucleic Acids Research. DOI: 10.1093/nar/gkag128
• Pastor et al. (2026). Manipulation of Alternative Splicing of IKZF1 Elicits Distinct Gene Regulatory Responses in T Cells
  Cells. DOI: 10.3390/cells15030221
• Radic-Sarikas et al. (2026). Mevalonate pathway activation in Ewing sarcoma reveals a 3D-specific synergy between statins and BCL-xL inhibition
  Molecular Therapy Oncology. DOI: 10.1016/j.omton.2026.201229
• Shtolz et al. (2026). Hypoxia leads to reduced mito-nuclear gene expression and increased mtDNA transcriptional pausing in human cells
  Communications Biology. DOI: 10.1038/s42003-025-09457-y
• Silvane et al. (2026). BCL11B targeting in tumor CD8+ T cells amplifies anti-tumor response by blocking exhaustion while promoting stemness and cytotoxicity
  DOI: 10.64898/2026.08.03.742578
• Song et al. (2026). GEfetch2R: fetching single-cell/bulk RNA-seq data from public repositories to R and benchmarking the subsequent format conversion tools
  GigaScience. DOI: 10.1093/gigascience/giag039
• Wang et al. (2026). Predictive prioritization of enhancers associated with pancreatic disease risk
  Cell Genomics. DOI: 10.1016/j.xgen.2025.101040
• Anton et al. (2025). Cervicovaginal microbiome alters transcriptomic and chromatin accessibility signatures across cervicovaginal epithelial barriers
  Microbiome. DOI: 10.1186/s40168-025-02223-6
• Cho et al. (2025). OncoDB 2.0: a comprehensive platform for integrated pan-cancer omics analysis
  Nucleic Acids Research. DOI: 10.1093/nar/gkaf952
• Cho et al. (2025). Targeting eRNA‐Producing Super‐Enhancers Regulates TNFα Expression and Mitigates Chronic Inflammation in Mice and Patient‐Derived Immune Cells
  Advanced Science. DOI: 10.1002/advs.202505214
• Cingaram et al. (2025). Enhancing transcriptome mapping with rapid PRO-seq profiling of nascent RNA
  Molecular Cell. DOI: 10.1016/j.molcel.2025.06.029
• Dong et al. (2025). MTD: A cloud-based omics database and interactive platform for Myceliophthora thermophila
  Synthetic and Systems Biotechnology. DOI: 10.1016/j.synbio.2025.04.001
• Escobedo-Muñoz et al. (2025). How far are we from the era of big data in transcriptomics? Lessons from the bacterial data in GEO
  Briefings in Bioinformatics. DOI: 10.1093/bib/bbaf560
• Favaro et al. (2025). Quantification of intrinsic regulatory factors refines human hematopoietic progenitor definitions and reveals early erythroid lineage priming
  Cell Reports. DOI: 10.1016/j.celrep.2025.115913
• Gauberg et al. (2025). Spinal motor neuron development and metabolism are transcriptionally regulated by nuclear factor IA
  Science Advances. DOI: 10.1126/sciadv.adu3346
• Kananen et al. (2025). Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes
  Bioinformatics Advances. DOI: 10.1093/bioadv/vbaf039
• Lee et al. (2025). Epigenomic profiling of papillary thyroid carcinoma reveals distinct subtypes with clinical implications
  npj Precision Oncology. DOI: 10.1038/s41698-025-00932-7
• LeRoy et al. (2025). Atacformer: A transformer-based foundation model for analysis and interpretation of ATAC-seq data
  DOI: 10.1101/2025.11.03.685753
• Li et al. (2025). Integrative analysis of gene expression and chromatin dynamics multi-omics data in mouse models of bleomycin-induced lung fibrosis
  Epigenetics & Chromatin. DOI: 10.1186/s13072-025-00579-5
• Li et al. (2025). Heterogeneity of the tumor immune cell microenvironment revealed by single-cell sequencing in head and neck cancer
  Critical Reviews in Oncology/Hematology. DOI: 10.1016/j.critrevonc.2025.104677
• Matsushima et al. (2025). Zinc-finger proteins with a co-opted capsid domain anchor nucleosomes over transposon sequences
  DOI: 10.1101/2025.03.03.638093
• Mehta et al. (2025). Evolution of chromatin accessibility associated with traits of cichlid phenotypic diversity
  DOI: 10.1101/2025.10.09.681187
• Noorizadeh et al. (2025). YAP1 is a key regulator of EWS::FLI1-dependent malignant transformation upon IGF-1-mediated reprogramming of bone mesenchymal stem cells
  Cell Reports. DOI: 10.1016/j.celrep.2025.115381
• Patty et al. (2025). Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements
  Cell Reports. DOI: 10.1016/j.celrep.2025.115767
• Pulice and Meyerson (2025). Amplified dosage of the NKX2-1 lineage transcription factor controls its oncogenic role in lung adenocarcinoma
  Molecular Cell. DOI: 10.1016/j.molcel.2025.03.001
• Roth et al. (2025). PRMT5 activity sustains histone production to maintain genome integrity
  DOI: 10.1101/2025.07.03.663002
• Sigauke et al. (2025). Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages
  BMC Genomics. DOI: 10.1186/s12864-025-11568-z
• Tripplehorn et al. (2025). A direct interaction between the Chd1 CHCT domain and Rtf1 controls Chd1 distribution and nucleosome positioning on active genes
  Nucleic Acids Research. DOI: 10.1093/nar/gkaf816
• Xiang et al. (2025). MEF2D-expressing cancer precursors reprogram tissue-resident macrophages to support liver tumorigenesis
  Nature Cancer. DOI: 10.1038/s43018-025-01059-1
• Zheng et al. (2025). EAP: A versatile cloud-based platform for efficient quantitative analysis of large-scale ChIP/ATAC-seq datasets
  Computational and Structural Biotechnology Journal. DOI: 10.1016/j.csbj.2025.11.026
• Danko et al. (2023). Evolution of promoter-proximal pausing enabled a new layer of transcription control
  DOI: 10.21203/rs.3.rs-2679520/v1
• Luo et al. (2023). Epiblast-like stem cells established by Wnt/β-catenin signaling manifest distinct features of formative pluripotency and germline competence
  Cell Reports. DOI: 10.1016/j.celrep.2023.112021
• 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
• Singh et al. (2023). Cohesin regulates alternative splicing
  Science Advances. DOI: 10.1126/sciadv.ade3876
• Abadie et al. (2022). Flexible and scalable control of T cell memory by a reversible epigenetic switch
  DOI: 10.1101/2022.12.31.521782
• 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
• 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
• 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
• 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
• 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
• Wolpe et al. (2022). Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling
  DOI: 10.1101/2022.12.08.519600
• 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
• 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
• Gharavi et al. (2021). Embeddings of genomic region sets capture rich biological associations in low dimensions
  Bioinformatics. DOI: 10.1093/bioinformatics/btab439
• 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
• Hasegawa et al. (2021). Clonal inactivation of telomerase promotes accelerated stem cell differentiation
  bioRxiv. DOI: 10.1101/2021.04.28.441728
• Mölder et al. (2021). Sustainable data analysis with Snakemake
  F1000Research. DOI: 10.12688/f1000research.29032.2
• 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
• Shahin et al. (2021). Germline biallelic mutation affecting the transcription factor Helios causes pleiotropic defects of immunity
  Science Immunology. DOI: 10.1126/sciimmunol.abe3981
• Smith et al. (2021). PEPPRO: quality control and processing of nascent RNA profiling data
  Genome Biology. DOI: 10.1186/s13059-021-02349-4
• 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
• Weber et al. (2021). Transient rest restores functionality in exhausted CAR-T cells through epigenetic remodeling
  Science. DOI: 10.1126/science.aba1786
• 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
• 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
• 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
• Liu (2020). Clinical implications of chromatin accessibility in human cancers
  DOI: 10.18632/oncotarget.27584
• 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
• Stolarczyk et al. (2020). Refgenie: a reference genome resource manager
  GigaScience. DOI: 10.1093/gigascience/giz149
• Wang et al. (2020). Interdependence between histone marks and steps in Pol II transcription
  DOI: 10.1101/2020.04.08.032730
• Zhou et al. (2020). CATA: a comprehensive chromatin accessibility database for cancer
  bioRxiv. DOI: 10.1101/2020.05.16.099325
• 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:

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

[![PEP compatible](https://pepkit.github.io/img/PEP-compatible-green.svg)](https://pepkit.github.io)

Or HTML:

<a href="https://pepkit.github.io"><img src="https://pepkit.github.io/img/PEP-compatible-green.svg" alt="PEP compatible" style="float:left; margin:10px"></a>