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:

• 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:

• 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/rs.3.rs-2679520/v1
• 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:

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>