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

DOI10.5281/zenodo.4686335Zenodo4686335MaRDI QIDQ6687789

Dataset published at Zenodo repository.

Author name not available (Why is that?)

Publication date: 10 September 2020

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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 Blish_RCA_no_QC_filtering_project_to_multiple_panels.rds 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 ScanPY input files: input_data.zip The R script provides R code to regenerate the main paper Figures 2 to 7modulo some visual modifications performed in Inkscape. Provided R scripts are: ComputePairWiseDE_v2.R (Required code for pairwise DE computation) RCA_Figure_Reproduction.R Provided python Code for Scanpy analysis: RA_Scanpy.ipynb CITESeq_Scanpy.ipynb

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