This repository contains the code used to reproduce Figures 1–5 from the CellTag manuscript.
Figure1/ Code used to generate Figure 1.
Figure2/ Code used to generate Figure 2.
Figure3/ Code used to generate Figure 3.
Figure4/ Code used to generate Figure 4.
Figure5/ Code used to generate Figure 5.
script/preprocessing/ Preprocessing scripts for scRNA-seq, CellTag, and hashtag analyses.
script/analysis/ Downstream analysis scripts.
This repository is distributed under the MIT License. See the LICENSE file for details.
No installation is required. Users only need access to an R environment with the required packages installed (see Environment below).
Typical setup time: less than 10 minutes.
| Script | Produces |
|---|---|
Figure1/Figure 1c and 1d.R |
Fig 1c, 1d |
Figure1/figure 1h.R |
Fig 1h |
Figure1/Figure1_befg_figure2_cd_OA_function.R |
Fig 1b, 1e, 1f, 1g; Fig 2c, 2d (shared function) |
Figure2/Figure2_ef_clonal_size_distributions.R |
Fig 2e, 2f |
Figure3/Figure 3a.R |
Fig 3a |
Figure3/Figure3_d_Day0_PCA_inter_intra_dist.R |
Fig 3d |
Figure3/Figure3_bcegh_DVGs_3_data_function.R |
Fig 3b, 3c, 3e, 3g, 3h |
Figure3/Figure3_fi_GSEA_Day0_Unmani.R |
Fig 3f, 3i |
Figure3/Figure 3k.R |
Fig 3k |
Figure3/Figure3_lmno_human_ORA_PROGENy.R |
Fig 3l, 3m, 3n, 3o |
Figure4/Panel A.R |
Fig 4a |
Figure4/Panel B.R |
Fig 4b |
Figure4/Panel C.R |
Fig 4c |
Figure4/Figure4_f_edfig5_c.R |
Fig 4f; Extended Data Fig 5c |
Figure4/Figure4_g.R |
Fig 4g |
Figure5/Figure 5a.R |
Fig 5a |
Figure5/Figure 5c-5h.R |
Fig 5c–5h |
Figure5/Figure 5i.R |
Fig 5i |
Figure5/Fig5_j_DVG_MAGMA.R |
Fig 5j |
Expected runtime per script: approximately 5–30 minutes depending on the computational environment and dataset size.
Analyses were run under R 4.4.1 on macOS (x86_64-apple-darwin20).
Key packages:
| Package | Version |
|---|---|
| Seurat | 5.3.0 |
| ggplot2 | 4.0.0 |
| dplyr | 1.1.4 |
| tidyr | 1.3.1 |
| data.table | 1.17.0 |
| clusterProfiler | 4.12.6 |
| enrichplot | 1.24.4 |
| msigdbr | 25.1.1 |
| biomaRt | 2.60.1 |
| org.Hs.eg.db | 3.19.1 |
| pheatmap | 1.0.12 |
| patchwork | 1.3.0 |
Full session details available via sessionInfo().
Analysis code is archived on Zenodo: 10.5281/zenodo.20709794, corresponding to release v1.0-natsubmission of this repository.
Processed data are deposited on Zenodo: 10.5281/zenodo.20480987.