Galaxy |

Seurat RunTSNE (version 4.0.4+galaxy0)

Choose the format of the input:

Seurat RDS, Seurat H5, Single Cell Experiment RDS, Loom or AnnData

RDS file:

Select RDS file(s) with Seurat object for input

Choose the format of the output:

Seurat, Single Cell Experiment, AnnData or Loom

Genes to use:

A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs).

Advanced Options

Advanced Options 0

What it does

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.

Run t-SNE dimensionality reduction on selected features. Has the option of running in a reduced dimensional space (i.e. spectral tSNE, recommended), or running based on a set of genes.

Inputs

RDS object

Outputs

Seurat RDS object

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).