AnnData to Seurat conversion
1.0 (latest)

1.0 (latest)

3.0 (earliest)

Visit source

Download RO-Crate

Workflow Type: Galaxy

AnnData to Seurat format conversion (manually using Galaxy buttons)

Associated Tutorial

This workflows is part of the tutorial AnnData to Seurat conversion, available in the GTN

Features

Includes Galaxy Workflow Tests

Thanks to...

Tutorial Author(s): Julia Jakiela, Morgan Howells, Wendi Bacon

Tutorial Contributor(s): Helena Rasche, Pavankumar Videm, Mehmet Tekman

Workflow Author(s): Julia Jakiela, Morgan Howells

Funder(s): ELIXIR-UK: FAIR Data Stewardship training

SEEK ID: https://dev.workflowhub.eu/workflows/1255?version=2

Inputs

ID	Name	Description	Type
AnnData	AnnData	Input file in AnnData format	File

Steps

ID	Name	Description
1	Inspect AnnData	toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0
2	Inspect AnnData	toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0
3	Transpose	toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1
4	DropletUtils	toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2
5	Seurat Read10x	toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/3.2.3+galaxy0

Outputs

ID	Name	Description	Type
Inspect AnnData: obs	Inspect AnnData: obs	n/a	File
Inspect AnnData: X	Inspect AnnData: X	n/a	File
Converted Seurat object	Converted Seurat object	n/a	File

Version History

1.0 (latest) Created 16th Jul 2024 at 14:11 by Helena Rasche

Added/updated 4 files

Open master 048dda3

3.0 (earliest) Created 25th Jun 2024 at 11:16 by Helena Rasche

Added/updated 4 files

Frozen 3.0 d4d1e69

Creators and Submitter

Creators

Not specified

Submitter

Helena Rasche

Discussion Channel

GTN Matrix

Tool

DropletUtils

License

Creative Commons Attribution 4.0 International

Activity

Views: 213 Downloads: 87

Created: 25th Jun 2024 at 11:16

Last updated: 25th Jun 2024 at 11:16

AnnData to Seurat conversion 1.0 (latest) 1.0 (latest) 3.0 (earliest)