Workflows

These workflows are associated with Analysis of plant scRNA-Seq Data with Scanpy

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.

scRNA Plant Analysis

Last updated Nov 18, 2022

Launch in Tutorial Mode question
License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Parameter\nLeiden Resolution"];
  style 0 fill:#ded,stroke:#393,stroke-width:4px;
  1["ℹ️ Input Dataset\nSHR CSV.gz"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nWT CSV.gz"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Parameter\nMin Genes"];
  style 3 fill:#ded,stroke:#393,stroke-width:4px;
  4["ℹ️ Input Parameter\nMin Cells"];
  style 4 fill:#ded,stroke:#393,stroke-width:4px;
  5["ℹ️ Input Parameter\nMax Features"];
  style 5 fill:#ded,stroke:#393,stroke-width:4px;
  6["ℹ️ Input Parameter\nMax Lib Size"];
  style 6 fill:#ded,stroke:#393,stroke-width:4px;
  7["Import Anndata and loom"];
  1 -->|output| 7;
  8["Import Anndata and loom"];
  2 -->|output| 8;
  9["Manipulate AnnData"];
  7 -->|anndata| 9;
  8 -->|anndata| 9;
  10["Rename Batches"];
  9 -->|anndata| 10;
  680180f6-edfc-4f66-b265-7a63aaa22b39["Output\nscRNA Concatenated Datasets"];
  10 --> 680180f6-edfc-4f66-b265-7a63aaa22b39;
  style 680180f6-edfc-4f66-b265-7a63aaa22b39 stroke:#2c3143,stroke-width:4px;
  11["QC metrics"];
  10 -->|anndata| 11;
  12["Filter genes"];
  11 -->|anndata_out| 12;
  3 -->|output| 12;
  13["Plot Violin"];
  11 -->|anndata_out| 13;
  14["Filter Cells"];
  12 -->|anndata_out| 14;
  4 -->|output| 14;
  15["Filter Max Features"];
  14 -->|anndata_out| 15;
  5 -->|output| 15;
  16["Filter Max Library Size"];
  15 -->|anndata| 16;
  6 -->|output| 16;
  17["Save RAW"];
  16 -->|anndata| 17;
  18["Norm to 1e4"];
  17 -->|anndata| 18;
  19["Log1p"];
  18 -->|anndata_out| 19;
  20["Regress total counts"];
  19 -->|anndata_out| 20;
  21["Scale"];
  20 -->|anndata_out| 21;
  22["PCA"];
  21 -->|anndata_out| 22;
  23["Neighborhod"];
  22 -->|anndata_out| 23;
  24["UMAP"];
  23 -->|anndata_out| 24;
  25["Leiden"];
  24 -->|anndata_out| 25;
  0 -->|output| 25;
  48cf0465-84ba-461a-bdb9-61625626de42["Output\nscRNA with clusters Dataset"];
  25 --> 48cf0465-84ba-461a-bdb9-61625626de42;
  style 48cf0465-84ba-461a-bdb9-61625626de42 stroke:#2c3143,stroke-width:4px;
  26["Plot PCA batch"];
  24 -->|anndata_out| 26;
  27["Plot UMAP batch"];
  24 -->|anndata_out| 27;
  28["Plot UMAP leiden, batch"];
  25 -->|anndata_out| 28;
  29["Rename Clusters"];
  25 -->|anndata_out| 29;
  30["Complex DotPlot"];
  25 -->|anndata_out| 30;
  31["Complex DotPlot with new labels"];
  29 -->|anndata| 31;
  32["Plot UMAP with new labels"];
  29 -->|anndata| 32;
	

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
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on galaxy-upload Import at the top-right of the screen
  • 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”
  • 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