Published September 10, 2020
| Version 1
Dataset
Open
Robust clustering and interpretation of scRNA-seq data using reference component analysis
Description
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
Files
Memory_consumption.txt
Files
(6.5 GB)
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1.6 GB | Download |
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