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  1. Data from: Robust clustering and interpretation of scRNA-seq data using...

    • zenodo.org
    • data.niaid.nih.gov
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    Updated May 27, 2021
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    Florian Schmidt; Florian Schmidt; Bobby Ranjan; Bobby Ranjan (2021). Robust clustering and interpretation of scRNA-seq data using reference component analysis [Dataset]. http://doi.org/10.5281/zenodo.4021967
    Explore at:
    bin, txt, zipAvailable download formats
    Unique identifier
    https://doi.org/10.5281/zenodo.4021967
    Dataset updated
    May 27, 2021
    Dataset provided by
    Zenodohttp://zenodo.org/
    Authors
    Florian Schmidt; Florian Schmidt; Bobby Ranjan; Bobby Ranjan
    License

    Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
    License information was derived automatically

    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


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Share
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TwitterTwitter
Email
Click to copy link
Link copied
Close
Cite
Florian Schmidt; Florian Schmidt; Bobby Ranjan; Bobby Ranjan (2021). Robust clustering and interpretation of scRNA-seq data using reference component analysis [Dataset]. http://doi.org/10.5281/zenodo.4021967
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Data from: Robust clustering and interpretation of scRNA-seq data using reference component analysis

Related Article
Explore at:
bin, txt, zipAvailable download formats
Unique identifier
https://doi.org/10.5281/zenodo.4021967
Dataset updated
May 27, 2021
Dataset provided by
Zenodohttp://zenodo.org/
Authors
Florian Schmidt; Florian Schmidt; Bobby Ranjan; Bobby Ranjan
License

Attribution 4.0 (CC BY 4.0)https://creativecommons.org/licenses/by/4.0/
License information was derived automatically

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


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