Workflows

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, ...

End-to-End Tissue Microarray Analysis with Galaxy-ME

Associated Tutorial

This workflows is part of the tutorial GTN_Exemplar_002_TMA_workflow, available in the GTN

Thanks to...

Tutorial Author(s): Cameron Watson, [Allison ...

Mapping

Associated Tutorial

This workflows is part of the tutorial GTN - Sequence Analyses - Mapping (imported from uploaded file), available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Tutorial Author(s): [Joachim ...

This workflow begins from a set of genome assemblies of different samples, strains, species. The genome is first annotated with Funnanotate. Predicted proteins are furtner annotated with Busco. Next, 'ProteinOrtho' finds orthologs across the samples and makes orthogroups. Orthogroups where all samples are represented are extracted. Orthologs in each orthogroup are aligned with ClustalW. The alignments are cleaned with ClipKIT and the concatenation matrix is built using PhyKit. This can be used ...

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

Features

• Includes Galaxy Workflow Tests

Thanks to...

**Tutorial ...

Nucleoli segmentation and feature extraction using CellProfiler

Associated Tutorial

This workflows is part of the tutorial CP_pipeline_IDR_training, available in the GTN

Thanks to...

Tutorial Author(s): Beatriz Serrano-Solano, [Jean-Karim ...

This workflow creates an ESet object from scRNA metadata file and EBI SCXA retrieveal

Associated Tutorial

This workflows is part of the tutorial MuSiC-Deconvolution: Data generation | sc | matrix + ESet, available in the GTN

Features

• Uses subworkflows ...