AnnData to SingleCellExperiment (SCE) conversion

single-cell-scrna-data-ingest/anndata-to-singlecellexperiment--sce--conversion

Author(s)
Julia Jakiela, Morgan Howells
Version
1
Last updated
Feb 13, 2024
License
CC-BY-4.0
Tags

Features
Tutorial
Converting between common single cell data formats
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00205
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nAnnData"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nCell ID column"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["Inspect AnnData"];
  0 -->|output| 2;
  8b9200c2-96e6-40fa-a8e9-1e99638c733f["Output\nInspect AnnData: obs"];
  2 --> 8b9200c2-96e6-40fa-a8e9-1e99638c733f;
  style 8b9200c2-96e6-40fa-a8e9-1e99638c733f stroke:#2c3143,stroke-width:4px;
  3["Inspect AnnData"];
  0 -->|output| 3;
  9fc4ce5a-8384-484d-b1cd-c0f5137cf821["Output\nInspect AnnData: X"];
  3 --> 9fc4ce5a-8384-484d-b1cd-c0f5137cf821;
  style 9fc4ce5a-8384-484d-b1cd-c0f5137cf821 stroke:#2c3143,stroke-width:4px;
  4["Transpose"];
  3 -->|X| 4;
  5["DropletUtils"];
  4 -->|out_file| 5;
  6["DropletUtils Read10x"];
  1 -->|output| 6;
  2 -->|obs| 6;
  5 -->|barcodes_out| 6;
  5 -->|genes_out| 6;
  5 -->|matrix_out| 6;
  3256e23f-2026-407d-aa25-0f8c0f3ae3f7["Output\nConverted SCE object"];
  6 --> 3256e23f-2026-407d-aa25-0f8c0f3ae3f7;
  style 3256e23f-2026-407d-aa25-0f8c0f3ae3f7 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset AnnData
Input parameter Cell ID column

Outputs

From Output Label
Input parameter Cell ID column
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 Inspect AnnData
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 Inspect AnnData
toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0 DropletUtils Read10x

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on Import at the top-right of the screen
  • Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
3 40f55005d 2023-12-15 21:54:56 workflow tests
2 0ab6c5160 2023-12-15 21:44:56 remove old workflows
1 2a9fd3b3f 2023-12-13 20:56:32 anndata -> sce workflow tests

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-SingleCellExperiment-(SCE)-conversion.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows