基因标记检索和细胞注释工具使用指南
百创S3000-FFPE Demo数据
2026年5月19日
1.、环境配置
conda install -c conda-forge r-base=4.3.1
conda install -c conda-forge r-optparse=1.7.5
conda install -c conda-forge r-dplyr=1.1.2
conda install -c conda-forge r-tidyr=1.3.1
2、小工具使用指南
2.1 帮助信息
Rscript cell_marker_cli.R -h
Usage: Rscript cell_marker_cli.R –mode MODE [options]
BMKMANU Cell Marker Database CLI – 标记检索与细胞注释工具
Options:
-m MODE, –mode=MODE
运行模式: marker_search (标记检索) 或 celltype_anno (细胞注释) [required]
-s SPECIES, –species=SPECIES
物种 (默认: Human)
-t TISSUE, –tissue=TISSUE
组织 (可选, 默认不过滤)
-k MARKERS, –marker=MARKERS
标记基因, 多个用逗号分隔 (仅 marker_search 模式)
-g GENES, –genes=GENES
输入基因列表, 多个用逗号或换行分隔 (仅 celltype_anno 模式)
-o FILE, –output=FILE
输出文件路径 (CSV格式, 默认输出到控制台)
–top=N
细胞注释模式返回前N个结果 (默认: 20)
-d FILE, –data=FILE
MarkerGene数据文件路径 (默认: 脚本同目录下的 cell_marker_cli.txt)
–list-species
列出所有可用的物种
–list-tissues
列出指定物种下的所有组织
-v, –verbose
显示详细输出
-h, –help
Show this help message and exit
2.2 操作示例
3、分析结果
Rscript cell_marker_cli.R --mode celltype_anno --species Human --genes 'CD3D,CD19,CD68' ╔══════════════════════════════════════════════════════════════╗ ║BMKMANU Cell Marker Database - Command Line Tool ║ ╠══════════════════════════════════════════════════════════════╣ ║Mode 1: marker_search - 根据物种/组织/标记基因检索细胞类型 ║ ║Mode 2: celltype_anno - 根据输入基因列表预测细胞类型 ║ ╚══════════════════════════════════════════════════════════════╝ ═══════════════════════════════════════════════════════════════ 预测细胞类型 (Top 20) ═══════════════════════════════════════════════════════════════ 输入基因: 3 个 匹配基因: 3 个 (CD19, CD3D, CD68) ═══════════════════════════════════════════════════════════════
| 排名 | 细胞类型 | 组织 | 匹配数 | 匹配率 | 匹配基因 |
|---|---|---|---|---|---|
| 1 | Activated CD4+ T cell | Blood | 2 | 66.7% | CD19, CD3D |
| 2 | Macrophage | Blood | 2 | 66.7% | CD19, CD68 |
| 3 | Monocyte | Peripheral blood | 2 | 66.7% | CD19, CD68 |
| 4 | Myeloid cell | Bone marrow | 2 | 66.7% | CD68, CD19 |
| 5 | Natural killer cell | Blood | 2 | 66.7% | CD19, CD3D |
| 6 | T cell | Blood | 2 | 66.7% | CD3D, CD19 |
| 7 | Activated B cell | Blood | 1 | 33.3% | CD19 |
| 8 | Activated CD8+ T cell | Blood | 1 | 33.3% | CD3D |
| 9 | Activated macrophage | Brain | 1 | 33.3% | CD68 |
| 10 | Activated microglial cell | Brain | 1 | 33.3% | CD68 |
| 11 | Activated microglial cell | Hippocampus | 1 | 33.3% | CD68 |
| 12 | Aged memory B cell | Peripheral blood | 1 | 33.3% | CD19 |
| 13 | Antibody-secreting cell | Peripheral blood | 1 | 33.3% | CD19 |
| 14 | Atypical memory B cell | Peripheral blood | 1 | 33.3% | CD19 |
| 15 | Atypical memory B cell | Venous blood | 1 | 33.3% | CD19 |
| 16 | B cell | Airway | 1 | 33.3% | CD19 |
| 17 | B cell | Bile duct | 1 | 33.3% | CD3D |
| 18 | B cell | Bladder | 1 | 33.3% | CD19 |
| 19 | B cell | Blood | 1 | 33.3% | CD19 |
| 20 | B cell | Blood vessel | 1 | 33.3% | CD19 |
─────────────────────────────────────────────────────────────── Top 预测结果: #1 Activated CD4+ T cell (组织: Blood) - 匹配 2/3 基因 (66.7%) #2 Macrophage (组织: Blood) - 匹配 2/3 基因 (66.7%) #3 Monocyte (组织: Peripheral blood) - 匹配 2/3 基因 (66.7%) #4 Myeloid cell (组织: Bone marrow) - 匹配 2/3 基因 (66.7%) #5 Natural killer cell (组织: Blood) - 匹配 2/3 基因 (66.7%) ─────────────────────────────────────────────────────────────── ✅ 完成! 注意： 1. 脚本执行后，执行结果会打印到屏幕上 2. 如果想要结果重定向，指定参数-o即可 3. 结果只展示其中一种，其它操作示例客户可自行探索 4. 默认用脚本所在目录的cell_marker_cli.txt，当然客户也可自行配置
