Downstream Single-cell RNA Plant analysis with ScanPy

Associated Tutorial

This workflows is part of the tutorial Analysis of plant scRNA-Seq Data with Scanpy, available in the GTN

Thanks to...

Tutorial Author(s): Mehmet Tekman, [Beatriz ...

Associated Tutorial

This workflows is part of the tutorial Filter, plot, and explore single cell RNA-seq data with Seurat, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

Workflow Author(s): ...

Workflow for the first half of the "Bulk RNA Deconvolution with MuSiC" tutorial.

Associated Tutorial

This workflows is part of the tutorial Bulk RNA Deconvolution with MuSiC, available in the GTN

Features

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

Pseudobulk Analysis Workflow for Tutorial

Associated Tutorial

This workflows is part of the tutorial Pseudobulk Analysis with Decoupler and EdgeR, available in the GTN

Features

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

Workflow for the second half of the "Bulk RNA Deconvolution with MuSiC" tutorial.

Implements the "Estimation of cell type proportions with pre-grouping of cell types" section

Associated Tutorial

This workflows is part of the tutorial Bulk RNA Deconvolution with MuSiC, available in the GTN

Features

• Includes [Galaxy Workflow ...

Associated Tutorial

This workflows is part of the tutorial Removing the effects of the cell cycle, available in the GTN

Features

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

Associated Tutorial

This workflows is part of the tutorial Pre-processing of 10X Single-Cell RNA Datasets, available in the GTN

Features

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

Downstream Single-cell RNA analysis with RaceID

Associated Tutorial

This workflows is part of the tutorial Downstream Single-cell RNA analysis with RaceID, available in the GTN

Features

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

Single-cell quality control with scater

Associated Tutorial

This workflows is part of the tutorial Single-cell quality control with scater, available in the GTN

Features

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

Downstream Single-cell RNA Plant analysis with ScanPy

Associated Tutorial

This workflows is part of the tutorial Analysis of plant scRNA-Seq Data with Scanpy, available in the GTN

Features

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

Single-cell/nuclei pipeline for data derived from Oxford Nanopore

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

• preprocessing
• filtering
• concatenation
• dimension reduction
• batch correction (with Harmony and optionally Scanorama and MNC-correct)
• leiden clustering

• new SnapATAC2 version: from 2.5.3 to 2.6.4

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MARS-seq v2 preprocessing pipeline