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 ...

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 ...

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 ...

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 ...

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 ...

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): ...

Downstream Single-cell RNA Plant analysis with ScanPy

Associated Tutorial

This workflows is part of the tutorial scRNA Plant Analysis, available in the GTN

Thanks to...

Tutorial Author(s): Mehmet Tekman, Beatriz Serrano-Solano, ...

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 ...

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 ...

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 analysis with RaceID

Associated Tutorial

This workflows is part of the tutorial RaceID Workflow, available in the GTN

Thanks to...

Tutorial Author(s): Mehmet Tekman, Alex Ostrovsky ...

An analysis pipeline for Molecular Cartography data from Resolve Biosciences.

Spatial Transcriptomics

Pipeline for processing of 10xGenomics single cell rnaseq data

Galaxy workflow

Galaxy workflow

Galaxy workflow