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Seurat FilterCells (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
Subsets used to filter cells
Subsets used to filter cells 0
Comma-separated list of cell names to use as a subset.
Seurat, Single Cell Experiment, AnnData or Loom

What it does

This tool filters cells in a Seurat object.

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. Probably the one produced by Seurat create object.
  • Subset names. A list of attributes to subset on, colon separated (:).
  • Low thresholds. A minimum value for each of the attributes set in subset names, again, colon separated (:). Optional.
  • High thresholds. A maximum value for each of the attributes set in subset names, again, colon separated (:). Optional.
  • Cells to use. A list of cell names/idenfifiers to filter positively by.

Outputs

  • Seurat RDS object filtered according to the inputs.

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).