Single-cell quality control with scater

Associated Tutorial

This workflows is part of the tutorial Single-cell quality control with scater, available in the GTN

Features

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

Updated tool versions Aug 24 2022

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 Tests
• Includes a [Galaxy ...

Filter, Plot and Explore Single-cell RNA-seq Data

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 Tests

Thanks

...

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 ...

Downstream Single-cell RNA analysis with RaceID

Associated Tutorial

This workflows is part of the tutorial Downstream Single-cell RNA analysis with RaceID, available in the GTN

Features

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

Pre-processing of Single-Cell RNA Data

Associated Tutorial

This workflows is part of the tutorial Pre-processing of Single-Cell RNA Data, available in the GTN

Thanks to...

Tutorial Author(s): Mehmet Tekman, [Bérénice ...

Pre-processing of Single-Cell RNA Data

Associated Tutorial

This workflows is part of the tutorial Pre-processing of Single-Cell RNA Data, available in the GTN

Features

• Uses subworkflows

Thanks to...

Tutorial Author(s): [Mehmet ...

Associated Tutorial

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

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): ...

Associated Tutorial

This workflows is part of the tutorial Pre-processing of 10X Single-Cell RNA Datasets, available in the GTN

Features

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

Downstream Single-cell RNA Plant analysis with ScanPy

Associated Tutorial

This workflows is part of the tutorial Analysis of plant scRNA-Seq Data with Scanpy, available in the GTN

Thanks to...

Tutorial Author(s): Mehmet Tekman, [Beatriz ...

Downstream Single-cell RNA Plant analysis with ScanPy

Associated Tutorial

This workflows is part of the tutorial Analysis of plant scRNA-Seq Data with Scanpy, available in the GTN

Features

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

Pseudobulk Analysis Workflow for Tutorial

Associated Tutorial

This workflows is part of the tutorial Pseudobulk Analysis with Decoupler and EdgeR, available in the GTN

Features

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

Workflow for the first half of the "Bulk RNA Deconvolution with MuSiC" tutorial.

Associated Tutorial

This workflows is part of the tutorial Bulk RNA Deconvolution with MuSiC, available in the GTN

Features

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

Workflow for the second half of the "Bulk RNA Deconvolution with MuSiC" tutorial.

Implements the "Estimation of cell type proportions with pre-grouping of cell types" section

Associated Tutorial

This workflows is part of the tutorial Bulk RNA Deconvolution with MuSiC, available in the GTN

Features

• Includes [Galaxy Workflow ...

Associated Tutorial

This workflows is part of the tutorial Removing the effects of the cell cycle, available in the GTN

Features

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

This workflow uses the decoupler tool in Galaxy to generate pseudobulk counts from an annotated AnnData file obtained from scRNA-seq analysis. Following the pseudobulk step, differential expression genes (DEG) are calculated using the edgeR tool. The workflow also includes data sanitation steps to ensure smooth operation of edgeR and minimizing potential issues. Additionally, a Volcano plot tool is used to visualize the results after the DEG analysis.

Associated Tutorial

This workflows is part of the tutorial Evaluating Reference Data for Bulk RNA Deconvolution, available in the GTN

Features

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

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 ...

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 ...

Associated Tutorial

This workflows is part of the tutorial Pre-processing of 10X Single-Cell ATAC-seq Datasets, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): Pavankumar Videm

**Tutorial ...