| # ===================================================== | |
| # YuanSeq Snakemake Workflow Configuration | |
| # 对应 YuanSeq Shiny 应用的命令行可复现流程 | |
| # 路径相对于 workflow/ 目录 | |
| # ===================================================== | |
| # --- 输入数据 --- | |
| input: | |
| counts: "data/counts.csv" # Counts矩阵：首列=GeneID，其余列=样本counts | |
| design: "data/design.csv" # 实验设计：sample, group (Control/Treatment) | |
| deg_file: null # 可选：预计算DEG文件路径，若设置则跳过差异分析 | |
| # --- 差异分析参数 --- | |
| differential: | |
| method: "auto" # auto/limma/edgeR (auto: 样本>=3用limma，否则edgeR) | |
| pval_type: "padj" | |
| pval_cutoff: 0.05 | |
| log2fc_cutoff: 1.0 | |
| edgeR_dispersion: 0.1 | |
| # --- 物种与注释 --- | |
| species: "Mm" # Mm=小鼠, Hs=人类 | |
| kegg_species: "mmu" # KEGG: mmu/hsa | |
| # --- KEGG 富集 --- | |
| kegg: | |
| direction: "Up" # Up / Down / All | |
| pvalueCutoff: 0.05 | |
| qvalueCutoff: 0.2 | |
| # --- GO 富集 --- | |
| go: | |
| ontology: "ALL" # BP / MF / CC / ALL | |
| pvalueCutoff: 0.05 | |
| qvalueCutoff: 0.2 | |
| # --- GSEA (可选，需提供 gmt_file 后单独运行) --- | |
| gsea: | |
| enabled: false | |
| gmt_file: null # 如 "data/c2.cp.kegg.v7.5.1.symbols.gmt" | |
| pvalueCutoff: 0.05 | |
| minGSSize: 10 | |
| maxGSSize: 500 | |
| id_type: "SYMBOL" | |
| # --- 转录因子活性 --- | |
| tf_activity: | |
| enabled: true | |
| method: "ulm" # ulm / mlm / wsum / viper | |
| min_genes: 5 | |
| collectri_dir: "." # CollecTRI 网络文件目录，可设为 YuanSeq 项目根目录 | |
| # --- 火山图 --- | |
| volcano: | |
| point_size: 6 | |
| point_alpha: 0.7 | |
| y_axis: "pvalue" | |
| label_genes: [] | |
| # --- 输出 --- | |
| output: | |
| dir: "results" | |
| prefix: "yuanseq" | |