AnnData to SingleCellExperiment (SCE) conversion

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

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

Features

Tutorial
hands_on Converting between common single cell data formats
workflow Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl 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 question
galaxy-download Download
output
output
X
out_file
output
obs
barcodes_out
genes_out
matrix_out
ℹ️ Input Dataset
AnnData
ℹ️ Input Parameter
Cell ID column
Inspect AnnData
Inspect AnnData
Transpose
DropletUtils
DropletUtils Read10x
Output
Inspect AnnData: obs
Output
Inspect AnnData: X
Output
Converted SCE object

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 galaxy-upload 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