Workflow Type: Galaxy
Stable

Basic 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.
  • File

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
  • File
1k_gene_table #main/1k_gene_table n/a
  • File
Scanpy FindCluster on input dataset(s): Clusters AnnData #main/Scanpy FindCluster on input dataset(s): Clusters AnnData n/a
  • File
Scanpy RunUMAP on input dataset(s): UMAP object AnnData #main/Scanpy RunUMAP on input dataset(s): UMAP object AnnData n/a
  • File
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
_anonymous_output_3 #main/_anonymous_output_3 n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File
_anonymous_output_5 #main/_anonymous_output_5 n/a
  • File
marker_dot_plot #main/marker_dot_plot n/a
  • File
marker_table #main/marker_table n/a
  • File
processed_anndata_object #main/processed_anndata_object n/a
  • File
umap_cluster_plot #main/umap_cluster_plot n/a
  • File
umap_sample_plot #main/umap_sample_plot n/a
  • File

Version History

main @ 7581788 (latest) Created 30th May 2024 at 06:52 by Sarah Williams

Updated workflow versions for anndata version conflict bugfix


Frozen main 7581788

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
help Creators and Submitter
Creators
  • Sarah Williams
  • Mike Thang
  • Valentine Murigneaux
Submitter
Citation
Williams, S., Thang, M., & Murigneaux, V. (2023). {scRNAseq on galaxy workflows}.
License
Activity

Views: 2612   Downloads: 227

Created: 5th May 2023 at 07:50

Last updated: 30th May 2024 at 06:52

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Total size: 3.75 MB
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