EBI SCXA to AnnData (Scanpy) or Seurat Object
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Download RO-CrateCreates input file for Filter, Plot, Explore tutorial
Associated Tutorial
This workflows is part of the tutorial EBI SCXA to AnnData (Scanpy) or Seurat Object, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Julia Jakiela, Wendi Bacon
Workflow Author(s): Julia Jakiela
Funder(s): ELIXIR-UK: FAIR Data Stewardship training
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| SC-Atlas experiment accession | SC-Atlas experiment accession | EBI Single Cell Atlas accession for the experiment that you want to retrieve. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | EBI SCXA Data Retrieval | toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2 |
| 2 | Rename batch numbers | Changes the batch label from "1" to "N01" etc toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3 |
| 3 | Mito genes check | Shows how mitochondrial genes are annotated. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 |
| 4 | Rename cell metadata headers | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 |
| 5 | Create AnnData | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy9 |
| 6 | Seurat Read10x | toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/3.2.3+galaxy0 |
| 7 | AnnData Operations | toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy92 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Mito genes check | Mito genes check | n/a |
|
| AnnData object | AnnData object | n/a |
|
| Seurat object | Seurat object | n/a |
|
| Mito-counted AnnData for downstream analysis | Mito-counted AnnData for downstream analysis | n/a |
|
Version History
1.0 (latest) Created 16th Jul 2024 at 14:10 by Helena Rasche
Added/updated 4 files
Open
master2c930db
2.0 (earliest) Created 25th Jun 2024 at 11:10 by Helena Rasche
Added/updated 4 files
Frozen
2.0b75959b
Creators and Submitter
Views: 513 Downloads: 148
Created: 25th Jun 2024 at 11:10
Last updated: 25th Jun 2024 at 11:10
AttributionsNone
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