NCBI to Anndata

single-cell-scrna-ncbi-anndata/ncbi-to-anndata

Author(s)
Morgan Howells, Pavankumar Videm
Version
2
Last updated
Dec 6, 2024
License
CC-BY-4.0
Tags
name:single-cell
name:data-management

Features
Tutorial
Converting NCBI Data to the AnnData Format
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00206
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
output
output
output
output
output
output
output
output
anndata
anndata
anndata
anndata
anndata
anndata
anndata
anndata
anndata
anndata
anndata
anndata
anndata
anndata
anndata
anndata
anndata
anndata
anndata
anndata
anndata
obs
obs
obs
obs
outfile
outfile
outfile
outfile
out_file1
out_file1
out_file1
out_file1
out_file1
out_file1
anndata
out_file1
anndata
output_h5ad
output_h5ad
ℹ️ Input Dataset
GSM5353219_PA_PB1B_Pool_2_S24_L001_dge.txt
ℹ️ Input Dataset
GSM5353223_PA_PB2B_Pool_2_S26_L001_dge.txt
ℹ️ Input Dataset
GSM5353218_PA_PB1B_Pool_1_2_S74_L003_dge.txt
ℹ️ Input Dataset
GSM5353216_PA_PB1A_Pool_1_3_S50_L002_dge.txt
ℹ️ Input Dataset
GSM5353221_PA_PB2A_Pool_1_3_S25_L001_dge.txt
ℹ️ Input Dataset
GSM5353215_PA_AUG_PB_1B_S2_dge.txt
ℹ️ Input Dataset
GSM5353222_PA_PB2B_Pool_1_3_S52_L002_dge.txt
ℹ️ Input Dataset
GSM5353220_PA_PB1B_Pool_3_S51_L002_dge.txt
ℹ️ Input Dataset
GSM5353217_PA_PB1A_Pool_2_S107_L004_dge.txt
ℹ️ Input Dataset
GSM5353214_PA_AUG_PB_1A_S1_dge.txt
Import Anndata
Import Anndata
Import Anndata
Import Anndata
Import Anndata
Import Anndata
Import Anndata
Import Anndata
Import Anndata
Import Anndata
Manipulate AnnData
Manipulate AnnData
Manipulate AnnData
Manipulate AnnData
Manipulate AnnData
Manipulate AnnData
Manipulate AnnData
Manipulate AnnData
Manipulate AnnData
Manipulate AnnData
Manipulate AnnData
Inspect AnnData
Replace Text
Replace Text
Replace Text
Replace Text
Cut
Cut
Cut
Cut
Paste
Paste
Paste
Manipulate AnnData
Scanpy FilterCells
AnnData Operations
Inspect AnnData
Output
output_h5ad
Output
obs

Inputs

Input Label
Input dataset GSM5353219_PA_PB1B_Pool_2_S24_L001_dge.txt
Input dataset GSM5353223_PA_PB2B_Pool_2_S26_L001_dge.txt
Input dataset GSM5353218_PA_PB1B_Pool_1_2_S74_L003_dge.txt
Input dataset GSM5353216_PA_PB1A_Pool_1_3_S50_L002_dge.txt
Input dataset GSM5353221_PA_PB2A_Pool_1_3_S25_L001_dge.txt
Input dataset GSM5353215_PA_AUG_PB_1B_S2_dge.txt
Input dataset GSM5353222_PA_PB2B_Pool_1_3_S52_L002_dge.txt
Input dataset GSM5353220_PA_PB1B_Pool_3_S51_L002_dge.txt
Input dataset GSM5353217_PA_PB1A_Pool_2_S107_L004_dge.txt
Input dataset GSM5353214_PA_AUG_PB_1A_S1_dge.txt

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0 AnnData Operations
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0 Inspect AnnData

Tools

Tool Links
Cut1
Paste1
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.9.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.9+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+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
3 a7b0e92fa 2024-12-06 11:28:52 add updated workflow
2 5503254f3 2023-12-13 18:14:03 Update to a working worflow and change test files type to tabular
1 cd3728b55 2023-12-12 19:08:26 add workflow

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-ncbi-anndata/workflows/NCBI_to_Anndata.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