The workflow containes the step to perpare the data for and run Galaxy Infinium Human Methylation BeadChip tool that represents many popular algorithms for detecting somatic genetic alterations from genome and exome data

Associated Tutorial

This workflows is part of the tutorial Infinium Human Methylation BeadChip, available in the GTN

Features

...

Identification of the binding sites of the Estrogen receptor

Associated Tutorial

This workflows is part of the tutorial Identification of the binding sites of the Estrogen receptor, available in the GTN

Thanks to...

Tutorial Author(s): Friederike Dündar, ...

Identification of the binding sites of the Estrogen receptor

Associated Tutorial

This workflows is part of the tutorial Identification of the binding sites of the Estrogen receptor, available in the GTN

Thanks to...

Tutorial Author(s): Friederike Dündar, ...

Associated Tutorial

This workflows is part of the tutorial Formation of the Super-Structures on the Inactive X, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): Friederike Dündar, ...

Hi-C analysis of Drosophila melanogaster cells using HiCExplorer

Associated Tutorial

This workflows is part of the tutorial Hi-C analysis of Drosophila melanogaster cells using HiCExplorer, available in the GTN

Thanks to...

Tutorial Author(s): Joachim Wolff, ...

Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)

Associated Tutorial

This workflows is part of the tutorial Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1), available in the GTN

Features

• Includes [Galaxy Workflow ...

atac-seq

Associated Tutorial

This workflows is part of the tutorial ATAC-Seq data analysis, available in the GTN

Thanks to...

Tutorial Author(s): Lucille Delisle, Maria Doyle, [Florian ...

DNA Methylation data analysis

Associated Tutorial

This workflows is part of the tutorial DNA Methylation data analysis, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Tutorial Author(s): [Joachim ...

CUT&RUN workflow used in GTN

Associated Tutorial

This workflows is part of the tutorial CUT&RUN data analysis, available in the GTN

Features

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

This Workflow takes a dataset collection of single-cell ATAC-seq fragments and performs:

• preprocessing
• filtering
• concatenation
• dimension reduction
• batch correction
• leiden clustering

Associated Tutorial

This workflows is part of the tutorial Multi-sample batch correction with Harmony and SnapATAC2, available in the GTN ...

Workflow of Tutorial "Single-cell ATAC-seq standard processing with SnapATAC2". This workflow takes a fragment file as input and performs the standard steps of scATAC-seq analysis: filtering, dimension reduction, embedding and visualization of marker genes with SnapATAC2. In an alternative step, the fragment file can also be generated from a BAM file.

Associated Tutorial

This workflows is part of the tutorial [Single-cell ATAC-seq standard processing with ...

Workflow for Single-cell ATAC-seq standard processing with SnapATAC2. This workflow takes a fragment file as input and performs the standard steps of scATAC-seq analysis: filtering, dimension reduction, embedding and visualization of marker genes with SnapATAC2. Finally, the clusters are manually annotated with the help of marker genes. In an alternative step, the fragment file can also be generated from a BAM file.

• newer Version: Updated SnapATAC2 version from 2.5.3 to 2.6.4