IDEAS home Printed from https://ideas.repec.org/a/plo/pcbi00/1008978.html
   My bibliography  Save this article

scHiCTools: A computational toolbox for analyzing single-cell Hi-C data

Author

Listed:
  • Xinjun Li
  • Fan Feng
  • Hongxi Pu
  • Wai Yan Leung
  • Jie Liu

Abstract

Single-cell Hi-C (scHi-C) sequencing technologies allow us to investigate three-dimensional chromatin organization at the single-cell level. However, we still need computational tools to deal with the sparsity of the contact maps from single cells and embed single cells in a lower-dimensional Euclidean space. This embedding helps us understand relationships between the cells in different dimensions, such as cell-cycle dynamics and cell differentiation. We present an open-source computational toolbox, scHiCTools, for analyzing single-cell Hi-C data comprehensively and efficiently. The toolbox provides two methods for screening single cells, three common methods for smoothing scHi-C data, three efficient methods for calculating the pairwise similarity of cells, three methods for embedding single cells, three methods for clustering cells, and a build-in function to visualize the cells embedding in a two-dimensional or three-dimensional plot. scHiCTools, written in Python3, is compatible with different platforms, including Linux, macOS, and Windows.Author summary: Single-cell Hi-C contact maps describe the numbers of interactions among genomic loci across the entire genome, and provide researchers 3D chromatin organization in each cell. There are growing demands for an easy and fast way to analyze and visualize single-cell Hi-C data, and analyzing single-cell Hi-C data exposes several inherent data analysis challenges. To move beyond existing computational tools and methods to analyze and visualize single-cell Hi-C data, we present a software package, scHiCTools, which is implemented in Python. The software package provides researchers a collection of methods to investigate the cell-to-cell similarity based on their 3D chromatin organization, cluster cells into groups accordingly, and visualize cells in two-dimensional or three-dimensional scatter plots. In this paper, we provide an overview of scHiCTools’ structure and capabilities. We then apply scHiCTools to several single-cell Hi-C datasets to benchmark the performance of the methods provided in our toolbox, and present some plots generated using the software package.

Suggested Citation

  • Xinjun Li & Fan Feng & Hongxi Pu & Wai Yan Leung & Jie Liu, 2021. "scHiCTools: A computational toolbox for analyzing single-cell Hi-C data," PLOS Computational Biology, Public Library of Science, vol. 17(5), pages 1-14, May.
    • Handle: RePEc:plo:pcbi00:1008978
    DOI: 10.1371/journal.pcbi.1008978
    as

    Download full text from publisher

    File URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008978
    Download Restriction: no
    File URL: https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008978&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pcbi.1008978?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Bo Wang & Armin Pourshafeie & Marinka Zitnik & Junjie Zhu & Carlos D. Bustamante & Serafim Batzoglou & Jure Leskovec, 2018. "Network enhancement as a general method to denoise weighted biological networks," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
    2. Samuel Collombet & Noémie Ranisavljevic & Takashi Nagano & Csilla Varnai & Tarak Shisode & Wing Leung & Tristan Piolot & Rafael Galupa & Maud Borensztein & Nicolas Servant & Peter Fraser & Katia Ancel, 2020. "Parental-to-embryo switch of chromosome organization in early embryogenesis," Nature, Nature, vol. 580(7801), pages 142-146, April.
    3. Lawrence Hubert & Phipps Arabie, 1985. "Comparing partitions," Journal of Classification, Springer;The Classification Society, vol. 2(1), pages 193-218, December.
    4. Ilya M. Flyamer & Johanna Gassler & Maxim Imakaev & Hugo B. Brandão & Sergey V. Ulianov & Nezar Abdennur & Sergey V. Razin & Leonid A. Mirny & Kikuë Tachibana-Konwalski, 2017. "Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition," Nature, Nature, vol. 544(7648), pages 110-114, April.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Miriam Aparicio, 2021. "Resiliency and Cooperation or Regarding Social and Collective Competencies for University Achievement. An Analysis from a Systemic Perspective," European Journal of Social Sciences Education and Research Articles, Revistia Research and Publishing, vol. 8, ejser_v8_.
    2. Yunpeng Zhao & Qing Pan & Chengan Du, 2019. "Logistic regression augmented community detection for network data with application in identifying autism‐related gene pathways," Biometrics, The International Biometric Society, vol. 75(1), pages 222-234, March.
    3. Wu, Han-Ming & Tien, Yin-Jing & Chen, Chun-houh, 2010. "GAP: A graphical environment for matrix visualization and cluster analysis," Computational Statistics & Data Analysis, Elsevier, vol. 54(3), pages 767-778, March.
    4. José E. Chacón, 2021. "Explicit Agreement Extremes for a 2 × 2 Table with Given Marginals," Journal of Classification, Springer;The Classification Society, vol. 38(2), pages 257-263, July.
    5. F. Marta L. Di Lascio & Andrea Menapace & Roberta Pappadà, 2024. "A spatially‐weighted AMH copula‐based dissimilarity measure for clustering variables: An application to urban thermal efficiency," Environmetrics, John Wiley & Sons, Ltd., vol. 35(1), February.
    6. Yifan Zhu & Chongzhi Di & Ying Qing Chen, 2019. "Clustering Functional Data with Application to Electronic Medication Adherence Monitoring in HIV Prevention Trials," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 11(2), pages 238-261, July.
    7. Irene Vrbik & Paul McNicholas, 2015. "Fractionally-Supervised Classification," Journal of Classification, Springer;The Classification Society, vol. 32(3), pages 359-381, October.
    8. Maurizio Vichi & Carlo Cavicchia & Patrick J. F. Groenen, 2022. "Hierarchical Means Clustering," Journal of Classification, Springer;The Classification Society, vol. 39(3), pages 553-577, November.
    9. Batool, Fatima & Hennig, Christian, 2021. "Clustering with the Average Silhouette Width," Computational Statistics & Data Analysis, Elsevier, vol. 158(C).
    10. Patrick D. Shay & Stephen S. Farnsworth Mick, 2017. "Clustered and distinct: a taxonomy of local multihospital systems," Health Care Management Science, Springer, vol. 20(3), pages 303-315, September.
    11. Roberto Rocci & Stefano Antonio Gattone & Roberto Di Mari, 2018. "A data driven equivariant approach to constrained Gaussian mixture modeling," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 12(2), pages 235-260, June.
    12. Wan-Lun Wang, 2019. "Mixture of multivariate t nonlinear mixed models for multiple longitudinal data with heterogeneity and missing values," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 28(1), pages 196-222, March.
    13. Matthijs Warrens, 2010. "Inequalities Between Kappa and Kappa-Like Statistics for k×k Tables," Psychometrika, Springer;The Psychometric Society, vol. 75(1), pages 176-185, March.
    14. Redivo, Edoardo & Nguyen, Hien D. & Gupta, Mayetri, 2020. "Bayesian clustering of skewed and multimodal data using geometric skewed normal distributions," Computational Statistics & Data Analysis, Elsevier, vol. 152(C).
    15. Jerzy Korzeniewski, 2016. "New Method Of Variable Selection For Binary Data Cluster Analysis," Statistics in Transition New Series, Polish Statistical Association, vol. 17(2), pages 295-304, June.
    16. Zhu, Xuwen & Melnykov, Volodymyr, 2018. "Manly transformation in finite mixture modeling," Computational Statistics & Data Analysis, Elsevier, vol. 121(C), pages 190-208.
    17. Amiri, Babak & Karimianghadim, Ramin, 2024. "A novel text clustering model based on topic modelling and social network analysis," Chaos, Solitons & Fractals, Elsevier, vol. 181(C).
    18. Li, Pai-Ling & Chiou, Jeng-Min, 2011. "Identifying cluster number for subspace projected functional data clustering," Computational Statistics & Data Analysis, Elsevier, vol. 55(6), pages 2090-2103, June.
    19. A van Giessen & K G M Moons & G A de Wit & W M M Verschuren & J M A Boer & H Koffijberg, 2015. "Tailoring the Implementation of New Biomarkers Based on Their Added Predictive Value in Subgroups of Individuals," PLOS ONE, Public Library of Science, vol. 10(1), pages 1-14, January.
    20. Guang Ouyang & Dipak K. Dey & Panpan Zhang, 2020. "Clique-Based Method for Social Network Clustering," Journal of Classification, Springer;The Classification Society, vol. 37(1), pages 254-274, April.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pcbi00:1008978. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.