Workflows

This is the workflow for the Batch Correction and Integration tutorial if you use Seurat.

Associated Tutorial

This workflows is part of the tutorial Batch Correction and Integration with Seurat or Scanpy, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

Workflow for GTN tutorial on single-cell batch correction, using the Scanpy pipeline with Harmony.

Associated Tutorial

This workflows is part of the tutorial Batch Correction and Integration with Seurat or Scanpy, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

A comprehensive Galaxy workflow for the end-to-end analysis of spatial data, featuring automated QC, clustering, spatial statistics, cell type annotation, and cell-cell communication.

This workflow performs retrieval of SRA metadata tables and FASTQ sequence files from input BioProject IDs.

This workflow performs colour deconvolution and automated thresholding to quantify stained area in brightfield histological images (MT, IHC). It accepts whole slides or pre-cropped ROIs.

Associated Tutorial

This workflows is part of the tutorial Quantitative Analysis of Histological Staining Using Color Deconvolution, available in the GTN ...

Post-curation processing workflow for VGP assemblies. Takes a curated AGP file and combined haplotype FASTA, splits by haplotype, applies curation, assigns chromosome names, renames and reorients hap2 to match hap1, then generates QC outputs including Compleasm, Pretext maps, telomere analysis, and coverage tracks.

This workflow performs colour deconvolution and automated thresholding to quantify stained area in brightfield histological images (MT, IHC). It accepts whole slides or pre-cropped ROIs.

Metaproteomics 101 tutorial

Associated Tutorial

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

Features

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

This WF applies Flexynesis on BRCA data from Metabric for a classification task

Associated Tutorial

This workflows is part of the tutorial Modeling Breast Cancer Subtypes with Flexynesis, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

Regression in Machine Learning

Associated Tutorial

This workflows is part of the tutorial Regression in Machine Learning, available in the GTN

Features

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