Robust clustering and interpretation of scRNA-seq data using reference component analysis

Datasets and Code accompanying the new release of RCA, RCA2. The R-package for RCA2 is available at GitHub: https://github.com/prabhakarlab/RCAv2/ The datasets included here are: Datasets required for a characterization of batch effects: merged_rna_seurat.rds de_list.rds mergedRCAObj.rds merged_rna_integrated.rds 10X_PBMCs.RDS: Processed 10X PBMC data RCA2 object (10X PBMC example data sets ) NBM_RDS_Files.zip: Several RDS files containing RCA2 object of Normal Bone Marrow (NBM) data, umap coordinates, doublet finder results and metadata information (Normal Bone Marrow use case) Dataset used for the Covid19 example: blish_covid.seu.rds rownames_of_glocal_projection_immune_cells.txt Data sets used to outline the ability of supervised clustering to detect disease states: 809653.seurat.rds blish_covid.seu.rds Performance benchmarking results: Memory_consumption.txt rca_time_list.rds The R script provides R code to regenerate the main paper Figures 2 to 7 modulo some visual modifications performed in Inkscape. Provided R scripts are: ComputePairWiseDE_v2.R (Required code for pairwise DE computation) RCA_Figure_Reproduction.R <br>本数据集与代码配套于RCA及RCA2的新版本发布。RCA2的R包可从GitHub获取：https://github.com/prabhakarlab/RCAv2/ 本次收录的数据集如下： 1. 用于批次效应表征的数据集：merged_rna_seurat.rds、de_list.rds、mergedRCAObj.rds、merged_rna_integrated.rds 2. 10X_PBMCs.RDS：经预处理的10X外周血单个核细胞（PBMC, Peripheral Blood Mononuclear Cells）数据对应的RCA2对象（10X PBMC示例数据集） 3. NBM_RDS_Files.zip：内含多份RDS文件，涵盖正常骨髓（Normal Bone Marrow, NBM）数据的RCA2对象、UMAP降维坐标、双细胞检测结果及元数据信息（正常骨髓应用场景） 4. 用于新冠（COVID-19）示例分析的数据集：blish_covid.seu.rds、rownames_of_glocal_projection_immune_cells.txt 5. 用于演示监督聚类检测疾病状态能力的数据集：809653.seurat.rds、blish_covid.seu.rds 6. 性能基准测试结果文件：Memory_consumption.txt、rca_time_list.rds 本R脚本提供了复现论文主图2至7的代码，仅需在Inkscape中完成部分视觉微调即可。所提供的R脚本包括：ComputePairWiseDE_v2.R（成对差异表达分析所需代码）、RCA_Figure_Reproduction.R