A statistical framework for comparative isoform profiling across cell populations.
To get started, please visit Hypatia's vignette.
Hypatia (hy-pay-shuh) is a computational toolkit for the investigation of population-specific isoforms from long-read single-cell RNA-sequencing data, featuring three modes of differential analyses:
- Isoform usage: Identifies differential isoform usage shifts (DIUs).
- Isoform diversity: Detects differential isoform diversity events (DIVs) and performs entropy-based classifications.
- Isoform expression: Detects differentially expressed isoforms (DEIs) across groups of cells.
Hypatia is an R library available through Github.
if (!requireNamespace("devtools", quietly = TRUE)) {
install.packages("devtools")
}
devtools::install_github("gaolabtools/Hypatia")Requires R version 4.1 or higher.
If installation gives the "Bad credentials" error after using GitHub PAT, there is an expired or invalid Github token stored on your machine.
To update or remove the invalid token, use gitcreds::gitcredsset() or gitcreds::gitcreds_delete(). Then retry the installation.
For detailed documentation and tutorial, please visit Hypatia's vignette.
If you found Hypatia useful in your research, please cite our preprint:
Pan, T., Shiau, C. K., Lu, L., Wang, C., Wang, M., He, Y., Bhimaraj, A., Brat, D., Huse, J.,
Jessica Li, J., & Gao, R. (2026). Hypatia: Comparative Isoform Profiling Across Cell Populations
from Long-Read Single-Cell Transcriptomes. bioRxiv : the preprint server for biology,
2026.01.13.699341. https://doi.org/10.64898/2026.01.13.699341