mCanonicalTockySeq: Multidimensional Canonical Tocky Analysis of Temporal and Developmental Structure in Single-Cell Transcriptomes
Author: Dr Masahiro Ono
Date: 16 March 2026
Overview
mCanonicalTockySeq is an R package for analysing single-cell transcriptomes in systems where temporal progression and developmental progression occur simultaneously.
The package was developed around the Nr4a3-Tocky system, in which a Fluorescent Timer reporter provides an experimentally anchored readout of strong T-cell receptor (TCR) signalling history.
More generally, the framework constructs a shared canonical space constrained by biologically defined landmark populations, and then extracts temporal and developmental structure using experimentally anchored biological readouts.
Rather than assuming that time and development are orthogonal latent variables, mCanonicalTockySeq represents them jointly in a biologically informed canonical geometry.
Interactive visualisations
Example interactive visualisations of Nr4a3-Tocky temporal development in the thymus are available at:
GitHub Pages:
https://MonoTockyLab.github.io/Nr4a3-Tocky-3D-Models/
In the Nr4a3-Tocky thymocyte setting, mCanonicalTockySeq enables:
- reconstruction of Tocky-defined temporal progression
- simultaneous quantification of developmental progression toward CD4 and CD8 states
- identification of gene-associated developmental trajectories across Tocky Time
- projection of new datasets, including cross-species ortholog-translated data, into an experimentally anchored reference space
Installation
You can install the development version from GitHub:
remotes::install_github("MonoTockyLab/mCanonicalTockySeq")Availability and documentation
- GitHub repository: mCanonicalTockySeq
- Package website: https://monotockylab.github.io/mCanonicalTockySeq/index.html
Citation
If you use mCanonicalTockySeq in your research, please cite the associated manuscript and the R package.
bioRxiv preprint
For a detailed description of the biological applications and underlying methodology of mCanonicalTockySeq, please refer to the associated preprint:
Canonical Analysis of Fluorescent Timer-Anchored Transcriptomes Resolves Joint Temporal and Developmental Progression Nobuko Irie, Omnia Reda, Yorifumi Satou, Masahiro Ono bioRxiv (2026). DOI: to be updated
@article{Ono2026mCanonicalTocky,
author = {Irie, Nobuko and Reda, Omnia and Satou, Yorifumi and Ono, Masahiro},
title = {Canonical Analysis of Fluorescent Timer-Anchored Transcriptomes Resolves Joint Temporal and Developmental Progression},
year = {2026},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
doi = {to be updated},
url = {https://www.biorxiv.org}
}R package
@Manual{Ono2026mCanonicalTockySeq,
title = {mCanonicalTockySeq: Multidimensional Canonical Tocky Analysis of Temporal and Developmental Structure in Single-Cell Transcriptomes},
author = {Masahiro Ono},
year = {2026},
note = {R package version 0.1.0},
url = {https://github.com/MonoTockyLab/mCanonicalTockySeq}
} 
The Ono Lab (MonoTockyLab)
The Masahiro Ono Lab (MonoTockyLab) develops experimental and computational approaches to study immune cell dynamics, with a particular focus on the temporal regulation of gene expression in T cells.
The lab is known for the development of Tocky (Timer of Cell Kinetics and Activity), a platform that uses Fluorescent Timer proteins to analyse transcriptional and signalling dynamics in vivo at single-cell resolution. Our research integrates mouse genetics, immunology, flow cytometry, single-cell omics, and computational modelling.
Current research directions include:
- cancer immunology and immunotherapy
- temporal mechanisms of T-cell activation, differentiation, and tolerance
- Foxp3 transcriptional dynamics and their regulation in vivo
- computational methods for time-resolved single-cell analysis, including CanonicalTockySeq
Principal Investigator: Dr Masahiro Ono
Dr Ono is the creator of Tocky, spanning both its transgenic reporter systems and associated analytical frameworks.
