Seurat Filter, Plot and Exlore tutorial
1.0

Workflow Type: Galaxy

Associated Tutorial

This workflows is part of the tutorial Filter, plot, and explore single cell RNA-seq data with Seurat, available in the GTN

Features

Thanks to...

Workflow Author(s): Camila Goclowski, Julia Jakiela

Tutorial Author(s): Camila Goclowski

Tutorial Contributor(s): Pablo Moreno, Pavankumar Videm, Helena Rasche, Camila Goclowski, Wendi Bacon, Julia Jakiela, Björn Grüning, Saskia Hiltemann

gtn star logo followed by the word workflows

Steps

ID Name Description
0 EBI SCXA Data Retrieval toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2
1 Seurat Read10x toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/4.0.4+galaxy0
2 Plot toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_plot/seurat_plot/4.0.4+galaxy0
3 Seurat FilterCells toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_filter_cells/seurat_filter_cells/4.0.4+galaxy0
4 Seurat NormaliseData toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data/4.0.4+galaxy0
5 Seurat FindVariableGenes toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes/4.0.4+galaxy0
6 Seurat ScaleData toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_scale_data/seurat_scale_data/4.0.4+galaxy0
7 Seurat RunPCA toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca/4.0.4+galaxy0
8 Seurat FindNeighbours toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_neighbours/seurat_find_neighbours/4.0.4+galaxy0
9 Seurat FindClusters toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters/4.0.4+galaxy0
10 Seurat UMAP toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_umap/seurat_run_umap/4.0.4+galaxy0
11 Plot toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_plot/seurat_plot/4.0.4+galaxy0

Outputs

ID Name Description Type
matrix_mtx matrix_mtx n/a
  • File
genes_tsv genes_tsv n/a
  • File
design_tsv design_tsv n/a
  • File
barcode_tsv barcode_tsv n/a
  • File
rds_seurat_clusters rds_seurat_clusters n/a
  • File
rds_seurat_umap rds_seurat_umap n/a
  • File

Version History

1.0 (earliest) Created 9th Dec 2024 at 13:10 by Helena Rasche

Added/updated 4 files


Open master 34607d8
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Views: 86   Downloads: 25

Created: 9th Dec 2024 at 13:10

Last updated: 9th Dec 2024 at 13:10

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Total size: 145 KB
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