Workflows

CRISPR screen analysis

Associated Tutorial

This workflows is part of the tutorial CRISPR screen analysis, available in the GTN

Thanks to...

Tutorial Author(s): Maria Doyle, Kenji Fujihara, ...

This workflow generates a single cell matrix using Alevin.

Associated Tutorial

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

Thanks to...

Workflow Author(s): Julia Jakiela, Wendi Bacon

Tutorial Author(s): Wendi Bacon, ...

Associated Tutorial

This workflows is part of the tutorial Introduction to Image Analysis using Galaxy, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): Till Korten, Leonid Kostrykin

**Tutorial ...

AnnData to CDS format conversion (manually using Galaxy buttons). This workflow does not include renaming the column containing gene symbols.

Associated Tutorial

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

Features

• Includes [Galaxy Workflow ...

Associated Tutorial

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

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): Marisa Loach

Tutorial Author(s): ...

Essential genes detection with Transposon insertion sequencing

Associated Tutorial

This workflows is part of the tutorial Essential genes detection with Transposon insertion sequencing, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks

...

The present workflow allows to perform 2D spots/blobs detection on specific channel and stack of an image. Images will be directly fetched from IDR by including the IDs. A pre-processing steps with histogram normalization is performed before the blobs detection.

Associated Tutorial

This workflows is part of the tutorial Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines, ...

AnnData to Seurat 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

...

Structural and functional genome annotation with Funannotate

Associated Tutorial

This workflows is part of the tutorial Genome annotation with Funannotate, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

**Workflow ...

Associated Tutorial

This workflows is part of the tutorial Using BioImage.IO models for image analysis in Galaxy, available in the GTN

Features

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