scRNAseq_QCtoBasicProcessing
View on GitHub
Download RO-Crate
Run on GalaxyBasic processing of a QC-filtered Anndata Object. UMAP, clustering e.t.c
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| QCFilteredAnnDataObject | #main/QCFilteredAnnDataObject | An AnnData object that has already undergone basic QC filtering. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | Scanpy NormaliseData | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.9.3+galaxy0 |
| 2 | Scanpy FindVariableGenes | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.9.3+galaxy1 |
| 3 | Scanpy ScaleData | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.9.3+galaxy0 |
| 4 | Scanpy RunPCA | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.9.3+galaxy0 |
| 5 | Scanpy ComputeGraph | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.9.3+galaxy0 |
| 6 | Scanpy RunUMAP | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.9.3+galaxy0 |
| 7 | Scanpy FindCluster | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.9.3+galaxy0 |
| 8 | Scanpy FindMarkers | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.9.3+galaxy0 |
| 9 | Plot sample UMAP | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.9.3+galaxy0 |
| 10 | Plot cluster UMAP | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.9.3+galaxy0 |
| 11 | Plot Markers | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy2 |
| 12 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 |
| 13 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 |
| 14 | Cell data preview | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1 |
| 15 | Gene data preview | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| 1k_cell_table | #main/1k_cell_table | n/a |
|
| 1k_gene_table | #main/1k_gene_table | n/a |
|
| Scanpy FindCluster on input dataset(s): Clusters AnnData | #main/Scanpy FindCluster on input dataset(s): Clusters AnnData | n/a |
|
| Scanpy RunUMAP on input dataset(s): UMAP object AnnData | #main/Scanpy RunUMAP on input dataset(s): UMAP object AnnData | n/a |
|
| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
|
| _anonymous_output_3 | #main/_anonymous_output_3 | n/a |
|
| _anonymous_output_4 | #main/_anonymous_output_4 | n/a |
|
| _anonymous_output_5 | #main/_anonymous_output_5 | n/a |
|
| marker_dot_plot | #main/marker_dot_plot | n/a |
|
| marker_table | #main/marker_table | n/a |
|
| processed_anndata_object | #main/processed_anndata_object | n/a |
|
| umap_cluster_plot | #main/umap_cluster_plot | n/a |
|
| umap_sample_plot | #main/umap_sample_plot | n/a |
|
Version History
main @ 7581788 (latest) Created 30th May 2024 at 06:52 by Sarah Williams
Updated workflow versions for anndata version conflict bugfix
Frozen
main7581788
main @ a95a4ee Created 22nd Jun 2023 at 07:24 by Sarah Williams
counts matrix workflow doc, affiliations
Frozen
main
a95a4ee
master @ 76f52ed (earliest) Created 5th May 2023 at 07:50 by Sarah Williams
count and load
Frozen
master
76f52ed
Creators and SubmitterViews: 4199 Downloads: 417 Runs: 0
Created: 5th May 2023 at 07:50
Last updated: 30th May 2024 at 06:52
Tags AttributionsNone
Collections
scRNAseq processing...
Related items
Teams: QCIF Bioinformatics
Organizations: QCIF
The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Teams: Australian BioCommons, QCIF Bioinformatics, Pawsey Supercomputing Research Centre, Sydney Informatics Hub, Janis, Melbourne Data Analytics Platform (MDAP), Galaxy Australia
Web page: https://www.biocommons.org.au/
Working closely with researchers, the QCIF Bioinformatics team apply data management, processing, integration, analysis and visualisation techniques to maximise the potential value of biological and clinical data sets. QCIF Bioinformatics is a partner in the Australian BioCommons.
Space: Australian BioCommons
Public web page: https://www.qcif.edu.au/
This collection houses some scanpy-based scRNAseq workflows on galaxy Australia.
The aim of these workflows is to handle the routine ‘boring’ part of single cell RNAseq data processing. It will produces an ‘AnnData’ object, which can then be used as a base for downstream analysis – either within galaxy or outside of it. AnnData is a standard format used by the ‘scanpy’ python package.
These workflows represent just one way of processing data for a ‘typical’ scRNAseq experiment – there are many ...
