Workflows

Trajectory analysis using Monocle3, starting from AnnData

Associated Tutorial

This workflows is part of the tutorial Inferring single cell trajectories with Monocle3, available in the GTN

Features

• Includes Galaxy Workflow Tests

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AnnData to SCE format conversion (manually using Galaxy buttons)

Associated Tutorial

This workflows is part of the tutorial Converting between common single cell data formats, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks

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Generic workflow to perform Voronoi segmentation. Input requirements:

• Image: -- Preferably lighter objects on a darker background for the mask to work well. -- Format: .tiff, stored in planar RGB format, not interleaved (http://avitevet.com/uncategorized/when-to-use-it-interleaved-vs-planar-image-data-storage/).
• Seeds: -- White seeds on a black background -- Format: .tiff

Associated Tutorial

This workflows is part of the tutorial [Voronoi ...

Functional annotation of protein sequences

Associated Tutorial

This workflows is part of the tutorial Functional annotation of protein sequences, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): ...

Preparing and filtering gene and cell annotations files and expression matrix to be passed as input for Monocle

Associated Tutorial

This workflows is part of the tutorial Inferring single cell trajectories with Monocle3, available in the GTN

Thanks to...

Tutorial Author(s): [Julia ...

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 ...

Workflows for comparison of genes in annotated genomes

Associated Tutorial

This workflows is part of the tutorial Comparative gene analysis in unannotated genomes, available in the GTN

Thanks to...

Workflow Author(s): Anton Nekrutenko

Tutorial Author(s): Anton Nekrutenko ...

Workflow to assess nuclei segmentation by applying different Gaussian filtering values during image pre-processing.

Associated Tutorial

This workflows is part of the tutorial Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy, available in the GTN

Features

• Includes [Galaxy Workflow ...

Trajectory analysis using Monocle3, starting from 3 input files: expression matrix, gene and cell annotations

Associated Tutorial

This workflows is part of the tutorial Inferring single cell trajectories with Monocle3, available in the GTN

Thanks to...

Tutorial Author(s): [Julia ...

Associated Tutorial

This workflows is part of the tutorial GO Enrichment Analysis on Single-Cell RNA-Seq Data, available in the GTN

Features

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