Multisample Batch Correction with SnapATAC2 and Harmony 1.0
Visit source
Download RO-Crate
Run on GalaxyThis Workflow takes a dataset collection of single-cell ATAC-seq fragments and performs:
- preprocessing
- filtering
- concatenation
- dimension reduction
- batch correction
- leiden clustering
Associated Tutorial
This workflows is part of the tutorial Multi-sample batch correction with Harmony and SnapATAC2, available in the GTN
Features
- Includes a Galaxy Workflow Report
- Uses Galaxy Workflow Comments
Thanks to...
Workflow Author(s): Timon Schlegel
Tutorial Author(s): Timon Schlegel
Tutorial Contributor(s): Diana Chiang Jurado, Saskia Hiltemann, Timon Schlegel
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input MultiSample Collection | Input MultiSample Collection | n/a |
|
| chrom_sizes | chrom_sizes | n/a |
|
| gencode.v46.annotation.gtf.gz | gencode.v46.annotation.gtf.gz | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | pp.import_data | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 4 | metrics.tsse | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 5 | pl.tsse | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1 |
| 6 | pp.filter_cells | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 7 | pp.add_tile_matrix | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 8 | pp.select_features | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 9 | pp.scrublet | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 10 | pp.filter_doublets | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 11 | Extract element identifiers | toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 |
| 12 | Extract first dataset | __EXTRACT_DATASET__ |
| 13 | Select first | Show beginning1 |
| 14 | Filter collection | __FILTER_FROM_FILE__ |
| 15 | Concatenate AnnDatas | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0 |
| 16 | pp.select_features on all | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 17 | tl.spectral | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1 |
| 18 | tl.umap_no-batch-correction | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1 |
| 19 | pl.umap_no-batch-correction | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1 |
| 20 | pp.harmony | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 21 | pp.mnn_correct | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 22 | pp.scanorama | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_preprocessing/snapatac2_preprocessing/2.6.4+galaxy1 |
| 23 | tl.umap_batch-correction | Recalculates UMAP-embeddings and adds it under the key 'X_umap_harmony' toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1 |
| 24 | tl.umap_mnn-correct | Recalculates UMAP-embeddings and adds it under the key 'X_umap_harmony' toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1 |
| 25 | tl.umap_scanorama | Recalculates UMAP-embeddings and adds it under the key 'X_umap_harmony' toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1 |
| 26 | UMAP-plot of X_spectral_harmony | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1 |
| 27 | pp.knn | Recalculates UMAP-embeddings and adds it under the key 'X_umap_harmony' toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1 |
| 28 | UMAP-plot of X_spectral_mnn-correct | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1 |
| 29 | UMAP plot of X_spectral_scanorama | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1 |
| 30 | tl.leiden | Recalculates UMAP-embeddings and adds it under the key 'X_umap_harmony' toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_clustering/snapatac2_clustering/2.6.4+galaxy1 |
| 31 | UMAP-plot of Leiden Clusters | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| tsse-plots | tsse-plots | n/a |
|
| collection_without_first_entry | collection_without_first_entry | n/a |
|
| out_png | out_png | n/a |
|
| x_spectral_harmony | x_spectral_harmony | n/a |
|
| x_spectral_mnn-correct | x_spectral_mnn-correct | n/a |
|
| x_spectral_scanorma | x_spectral_scanorma | n/a |
|
| anndata_harmony_leiden | anndata_harmony_leiden | n/a |
|
Version History
master
Creators and Submitter
Views: 53 Downloads: 7 Runs: 0
Created: 2nd Jun 2025 at 10:58
AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
I'm a bot managed by @hexylena to upload workflows from the Galaxy Training Network to the WorkflowHub. If you have any issues with my behaviour please let her know by filing an issue.
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network
Web page: https://galaxyproject.org/
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
