Dataset

mono2tam() → AnnData

GBM Monocyte Differentiation

In vivo timestamping of monocyte infiltration and differentiation into Arg1⁺/Acp5⁺ TAMs in glioblastoma models via Zman-seq.

Data from: Kirschenbaum, D., Xie, K., Ingelfinger, F., Katzenelenbogen, Y., Abadie, K., Look, T., … & Amit, I. (2023). Time-resolved single-cell transcriptomics defines immune trajectories in glioblastoma. Cell. https://doi.org/10.1016/j.cell.2023.11.032

celegans() → AnnData

C. elegans Embryogenesis

A curated subset of the C. elegans AB lineage (333 cells) spanning three experimental time points, featuring single-cell representatives for each lineage node sampled to preserve original temporal distributions.

Data from: Jonathan S. Packer et al. ,A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution.Science365,eaax1971(2019). https://doi.org/10.1126/science.aax1971

simudata() → AnnData

Simulated Time-series Dataset

A synthetic time-series dataset of 5,000 cells and 500 genes generated via scDesign3, containing ground-truth time and transcriptomic velocities derived from time-dependent GAMLSS models.

Data from: ScDesign3(Song, D., Wang, Q., Yan, G. et al. scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics. Nat Biotechnol 42, 247–252 (2024). https://doi.org/10.1038/s41587-023-01772-1) and CellDyc(method).

gastrulation() → AnnData

Mouse Erythroid Maturation

An scRNA-seq dataset capturing the complete erythroid lineage specification during mouse gastrulation across eight experimental time points, ranging from hematoendothelial progenitors to Erythroid 3 cells.

Data from: Pijuan-Sala, B., Griffiths, J.A., Guibentif, C. et al. A single-cell molecular map of mouse gastrulation and early organogenesis. Nature 566, 490–495 (2019). https://doi.org/10.1038/s41586-019-0933-9

zebrafish() → AnnData

Zebrafish Embryogenesis

A curated subset of 2,341 cells from a zebrafish embryogenesis atlas, capturing the axial mesoderm lineage (notochord and prechordal plate) across 12 experimental time points (3.3–12 hpf).

Data from: Jeffrey A. Farrell et al. ,Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis.Science360,eaar3131(2018). https://doi.org/10.1126/science.aar3131

reprogramming_lineage() → AnnData

Mouse Reprogramming Lineage

A CellTagging lineage-traced dataset of 3,049 cells across six time points, capturing the direct reprogramming of MEFs into iEPs and distinguishing between successful and dead-end trajectories.

Data from: Biddy, B.A., Kong, W., Kamimoto, K. et al. Single-cell mapping of lineage and identity in direct reprogramming. Nature 564, 219–224 (2018). https://doi.org/10.1038/s41586-018-0744-4.