Dawnn benchmarking dataset: Heart cells processing and label simulation

This project is a collection of files to allow users to reproduce the model development and benchmarking in "Dawnn: single-cell differential abundance with neural networks" (Hall and Castellano, under review). Dawnn is a tool for detecting differential abundance in single-cell RNAseq datasets. It is available as an R package here. Please contact us if you are unable to reproduce any of the analysis in our paper. The files in this collection correspond to the benchmarking dataset based on single-cell RNAseq of heart cells. <br> FILES: Input data Dataset from: "Integrated multi-omic characterization of congenital heart disease". Nature 608 pp. 181-191 (2022). <strong>heart_barcodes.tsv.gz</strong> Cell barcode list <strong>heart_genes.tsv.gz </strong>Gene list <strong>heart_expression_matrix.mtx.gz</strong> Cell-by-gene expression matrix Data processing code <strong>process_heart_cells.R</strong> Generates benchmarking dataset from input data. (Reads <em>heart_barcodes.tsv.gz</em>, <em>heart_genes.tsv.gz</em>, and <em>heart_expression_matrix.mtx.gz</em>; Runs the standard Seurat pipeline; Saves the resulting Seurat dataset as <em>heart_tissue_cells.RDS</em> and the resulting cell labels as <em>benchmark_dataset_heart_data_type_labels.csv</em>) Resulting datasets <strong>heart_tissue_cells.RDS</strong> Seurat dataset generated by <em>process_heart_cells.R</em>. <strong>benchmark_dataset_heart_data_type_labels.csv </strong>Cell labels generated by <em>process_heart_cells.R</em>.

本项目包含一系列配套文件，旨在支持用户复现论文《Dawnn: 基于神经网络的单细胞差异丰度分析》（Hall与Castellano，待审稿）中所述的模型开发与基准测试流程。Dawnn是一款用于检测单细胞RNA测序（single-cell RNAseq）数据集差异丰度的工具，可通过本项目提供的R包获取。若您无法复现论文中的任一分析环节，请与我们联系。本项目中的文件对应基于心肌细胞单细胞RNA测序的基准测试数据集。

### 文件列表
#### 输入数据
数据集来源：《先天性心脏病的整合多组学表征》（Integrated multi-omic characterization of congenital heart disease），《自然》（*Nature*）608卷，第181-191页（2022年）。
- **heart_barcodes.tsv.gz**：细胞条形码列表
- **heart_genes.tsv.gz**：基因列表
- **heart_expression_matrix.mtx.gz**：细胞-基因表达矩阵

#### 数据处理代码
**process_heart_cells.R**：从输入数据生成基准测试数据集。（读取`heart_barcodes.tsv.gz`、`heart_genes.tsv.gz`与`heart_expression_matrix.mtx.gz`；运行标准Seurat分析流程；将生成的Seurat数据集保存为`heart_tissue_cells.RDS`，并将细胞标签保存为`benchmark_dataset_heart_data_type_labels.csv`）

#### 生成结果数据集
- **heart_tissue_cells.RDS**：由`process_heart_cells.R`生成的Seurat数据集
- **benchmark_dataset_heart_data_type_labels.csv**：由`process_heart_cells.R`生成的细胞标签文件