Figures

Jupyter notebook

Figures were generated by Jupyter notebook scripts. In order to install Jupyter notebook/lab, see jupyter.org. You need to change dir_rna and/or dir_atac to locate the merged Seurat object or final ArchRProject object you generated. The output files include PDF files that will be located at the directory of "pdf".

./
├── figure1_01_umap.ipynb
├── figure1_02_barplot.ipynb
├── figure2_01_umap.ipynb
├── figure2_02_dge.ipynb
├── figure3_01_umap.ipynb
├── figure3_02_boxplot.ipynb
├── figure3_03_dge_pairs.ipynb
├── figure4_01_umap.ipynb
├── figure4_02_dge.ipynb
├── figure5_01_umap.ipynb
├── figure5_02_barplot.ipynb
├── figure5_03_drug_effect.ipynb
├── figure_s1_01_dge.ipynb
├── figure_s2_01_barplot.ipynb
├── figure_s2_02_dge.ipynb
├── log
├── pdf
│   ├── ...
│   ├── barplot_er+bc-pairs_cluster_type_prop_rna.pdf
│   ├── ...
│   ├── heatmap_er+bc-pairs_control_vs_tamoxifen_Tumor_cells_zscore.pdf
│   ├── ...
│   ├── umap_er+bc-pairs_cluster_labels_rna.pdf
│   ├── umap_er+bc-pairs_cluster_types_rna.pdf
│   ├── umap_er+bc-pairs_log2fc_t47d_down_genes_rna.pdf
│   └── umap_er+bc-pairs_samples_rna.pdf
├── r
├── reference
├── txt
│   └── sessionInfo.txt
└── xlsx
    ├── ...
    └── er+bc-pairs_control_vs_tamoxifen_Tumor_cells.xlsx

The scRNA-seq pipeline and scATAC-seq pipeline are actively developed. Other single cell data analysis projects will use the current version with different parameters or upgraded version of these pipelines.