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Seurat RunPCA (version 4.0.4+galaxy0)
Seurat RDS, Seurat H5, Single Cell Experiment RDS, Loom or AnnData
Select RDS file(s) with Seurat object for input
Seurat, Single Cell Experiment, AnnData or Loom
File with gene names to scale/center. Default is all genes in object@data.
File with cell names to scale/center. Default is all cells in object@data.
Total Number of PCs to compute and store (20 by default). Less PCs might be faster, but will explain less variance.
Run PCA on reverse matrix (gene x cell; FALSE by default means cell x gene).

What it does

This tool runs a PCA dimensionality reduction.

Seurat is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. It is developed and maintained by the Satija Lab at NYGC. Seurat aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data.

Inputs

  • Seurat RDS object, normalised and scaled potentially.
  • Genes used to scale. File of gene names to scale/center. Default is all genes in object.
  • Principal components to compute. Total Number of PCs to compute and store (20 by default). Less PCs might be faster, but will explain less variance.
  • Use imputed. Boolean indicating whether to run PCA on imputed values or not.

Outputs

  • Seurat RDS object with PCA calculations and embeddings.
  • Embeddings on CSV file. File with a csv-format embeddings table with principal components by cell.
  • Loadings on CSV file. File with a csv-format loadings table with principal components by gene.
  • Standard deviation on CSV file. Contains principal components std. deviations.

Version history 4.0.0: Moves to Seurat 4.0.0, introducing a number of methods for merging datasets, plus the whole suite of Seurat plots. Pablo Moreno with funding from AstraZeneca.

3.2.3+galaxy0: Moves to Seurat 3.2.3 and introduce convert method, improving format interconversion support.

3.1.2_0.0.8: Update metadata parsing

3.1.1_0.0.7: Exposes perplexity and enables tab input.

3.1.1_0.0.6+galaxy0: Moved to Seurat 3.

Find clusters: removed dims-use, k-param, prune-snn.

2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski (GitHub drosofff) and Lea Bellenger (GitHub bellenger-l).

0.0.1: Initial contribution. Maria Doyle (GitHub mblue9).