scRNA Plant Analysis

single-cell-scrna-plant/main-workflow

Author(s)

Version
1
Last updated
Nov 18, 2022
License
None Specified, defaults to CC-BY-4.0
Tags
transcriptomics
single-cell

Features
Tutorial
Analysis of plant scRNA-Seq Data with Scanpy
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00207
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
output
output
anndata
anndata
anndata
anndata
anndata_out
output
anndata_out
anndata_out
output
anndata_out
output
anndata
output
anndata
anndata
anndata_out
anndata_out
anndata_out
anndata_out
anndata_out
anndata_out
anndata_out
output
anndata_out
anndata_out
anndata_out
anndata_out
anndata_out
anndata
anndata
ℹ️ Input Parameter
Leiden Resolution
ℹ️ Input Dataset
SHR CSV.gz
ℹ️ Input Dataset
WT CSV.gz
ℹ️ Input Parameter
Min Genes
ℹ️ Input Parameter
Min Cells
ℹ️ Input Parameter
Max Features
ℹ️ Input Parameter
Max Lib Size
Import Anndata and loom
Import Anndata and loom
Manipulate AnnData
Rename Batches
QC metrics
Filter genes
Plot Violin
Filter Cells
Filter Max Features
Filter Max Library Size
Save RAW
Norm to 1e4
Log1p
Regress total counts
Scale
PCA
Neighborhod
UMAP
Leiden
Plot PCA batch
Plot UMAP batch
Plot UMAP leiden, batch
Rename Clusters
Complex DotPlot
Complex DotPlot with new labels
Plot UMAP with new labels
Output
scRNA Concatenated Datasets
Output
scRNA with clusters Dataset

Inputs

Input Label
Input parameter Leiden Resolution
Input dataset SHR (CSV.gz)
Input dataset WT (CSV.gz)
Input parameter Min Genes
Input parameter Min Cells
Input parameter Max Features
Input parameter Max Lib Size

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0 Manipulate AnnData Rename Batches
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0 Plot Plot Violin
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0 Cluster, infer trajectories and embed Leiden
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0 Plot Plot PCA (batch)
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0 Plot Plot UMAP (batch)
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0 Plot Plot UMAP (leiden, batch)
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0 Plot Complex DotPlot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0 Plot Complex DotPlot with new labels
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0 Plot Plot UMAP with new labels

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands On: Importing a workflow
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
1 327fd2b84 2022-11-12 17:14:25 Making a single cell topics

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-plant/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows