Associated Tutorial

This workflows is part of the tutorial Converting NCBI Data to the AnnData Format, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a Galaxy Workflow Report ...

This 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 ...

Workflow associated with this training: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.html

Associated Tutorial

This workflows is part of the tutorial Combining single cell datasets after pre-processing, available in the GTN

Features

• Includes ...

Updated March 2024

Associated Tutorial

This workflows is part of the tutorial Combining single cell datasets after pre-processing, available in the GTN

Thanks to...

Workflow Author(s): Julia Jakiela, Wendi Bacon

Tutorial Author(s): Wendi Bacon ...

This workflow is for the training material: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_alevin/tutorial.html

Associated Tutorial

This workflows is part of the tutorial Generating a single cell matrix using Alevin, available in the GTN

Features

• Includes a [Galaxy Workflow ...

Creates input file for Filter, Plot, Explore tutorial

Associated Tutorial

This workflows is part of the tutorial Importing files from public atlases, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a [Galaxy Workflow ...

Workflow based on clustering 3K PBMCs with Scanpy tutorial

Associated Tutorial

This workflows is part of the tutorial Clustering 3K PBMCs with Scanpy, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a [Galaxy Workflow ...

Associated Tutorial

This workflows is part of the tutorial Understanding Barcodes, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a Galaxy Workflow Report ...

Workflow for this training: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html

Associated Tutorial

This workflows is part of the tutorial Filter, plot and explore single-cell RNA-seq data with Scanpy, available in the GTN

Features

• Includes [Galaxy Workflow ...

This workflow was built for the 2024 Bioinformatics Bootcamp at The Open University. It is meant to occur after the (universal) Filter, plot and explore tutorial to allow analysis of a single cluster.

This workflow was developed for the 2024 Bioinformatics Bootcamp at The Open University. It imports datasets from the EBI SCXA, reformats then, and analyses them similar to the Filter, plot and explore Galaxy tutorial.

Run velocyto to get loom with counts of spliced and unspliced. It will extract the 'barcodes' from the bundled outputs.