Skip to content
DraconiticResearch
Search Sources API
178,970 studies31 sourcesUpdated 36 min ago
PreprintCC BYbioRxiv

ATACofthesnake: A scalable framework for analyzing multifactorial and time course chromatin accessibility data

  • W. Deboutte1
  • A. Lenaerts
  • A. Salatino
  • T. Manke
  1. 11. Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
Read full textPDFDOICite

Abstract

Advances in sample extraction techniques, improvement of library preparation methods and the dramatic reduction in sequencing costs have made complex, multifactorial experimental design the de facto standard in epigenomic studies. In contrast to the plethora of tools, workflows and libraries available to analyze gene expression data, consolidated workflows for chromatin accessibility data are lacking and analysis of such data often occurs on an ad hoc basis. Here, a scalable end-to-end workflow, ATACofthesnake, is presented that simplifies analysis of multifactorial chromatin accessibility data considerably and provides a newly created framework to handle time series data reproducibly.

Related

  1. Genome-wide loss of chromatin accessibility coexists with selectively elevated RNA abundance in nutrient-starved U2OS cells
    X. Qi, S. A. Al Refaai, S. Muslinov +1
    bioRxivPreprintAll rights reservedFull textBioinformatics & computational biologybioRxiv
  2. Epi-PoreC: a nanopore-based method for simultaneous profiling of chromatin conformation, DNA methylation, and chromatin accessibility
    A. McKinlay, W. Zong, C. Pikaard
    bioRxivPreprintCC BYFull textGenetics & genomicsbioRxiv
  3. Single-nucleus chromatin accessibility time course of excisional wound repair in rat skin
    C. Chai, X. Ding, Y. Li +12
    bioRxivPreprintCC BY-NC-NDFull textBioinformatics & computational biologybioRxiv
  4. ChAI-Net learns a regulatory code for chromatin co-accessibility
    J. Lee, K. Zhang, E. Shurberg +2
    bioRxivPreprintCC BY-NCFull textGenetics & genomicsbioRxiv
  5. Genome-Wide Evolution of Lineage-Specific Chromatin Accessibility Links Regulatory Changes to Cichlid Phenotypic Diversity.
    Tarang K Mehta, Angela L Man, Graham Etherington +6
    Genome biology and evolutionPeer-reviewedCC BYFull textPlant biologyEurope PMC

Cite

BibTeXRIS
BibTeX
@misc{deboutte2026atacofthesnake,
  title = {{ATACofthesnake: A scalable framework for analyzing multifactorial and time course chromatin accessibility data}},
  author = {W. Deboutte and A. Lenaerts and A. Salatino and T. Manke},
  howpublished = {bioRxiv},
  year = {2026},
  month = sep,
  doi = {10.64898/2026.09.18.752590},
  url = {https://www.biorxiv.org/content/10.64898/2026.09.18.752590v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - ATACofthesnake: A scalable framework for analyzing multifactorial and time course chromatin accessibility data
AU  - W. Deboutte
AU  - A. Lenaerts
AU  - A. Salatino
AU  - T. Manke
PY  - 2026
DA  - 2026/09/18
PB  - bioRxiv
DO  - 10.64898/2026.09.18.752590
UR  - https://www.biorxiv.org/content/10.64898/2026.09.18.752590v1
AB  - Advances in sample extraction techniques, improvement of library preparation methods and the dramatic reduction in sequencing costs have made complex, multifactorial experimental design the de facto standard in epigenomic studies. In contrast to the plethora of tools, workflows and libraries available to analyze gene expression data, consolidated workflows for chromatin accessibility data are lacking and analysis of such data often occurs on an ad hoc basis. Here, a scalable end-to-end workflow, ATACofthesnake, is presented that simplifies analysis of multifactorial chromatin accessibility data considerably and provides a newly created framework to handle time series data reproducibly.
ER  -