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single-cell-ebi-gxa.yaml
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single-cell-ebi-gxa.yaml
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---
install_repository_dependencies: true
install_resolver_dependencies: true
install_tool_dependencies: false
tools:
- name: dropletutils_read_10x
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_utils_viz'
- name: dropletutils_empty_drops
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_utils_viz'
- name: gtf2gene_list
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_utils_viz'
- name: retrieve_scxa
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_get-scrna'
- name: hca_matrix_downloader
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_get-scrna'
- name: sc3_calc_biology
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_sc3_tools'
- name: sc3_calc_consens
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_sc3_tools'
- name: sc3_calc_dists
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_sc3_tools'
- name: sc3_calc_transfs
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_sc3_tools'
#
- name: sc3_estimate_k
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_sc3_tools'
- name: sc3_kmeans
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_sc3_tools'
- name: sc3_prepare
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_sc3_tools'
- name: anndata_ops
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_compute_graph
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_filter_cells
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_filter_genes
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_find_cluster
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_find_markers
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_find_variable_genes
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_normalise_data
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_parameter_iterator
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_plot_embed
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_plot_trajectory
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_read_10x
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_regress_variable
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_run_diffmap
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_run_dpt
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_run_fdg
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_run_paga
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_run_pca
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_run_tsne
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_run_umap
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_scale_data
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_integrate_combat
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_integrate_harmony
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_integrate_mnn
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_integrate_bbknn
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_plot_scrublet
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_multiplet_scrublet
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: scanpy_integrate_bbknn
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scanpy_tools'
- name: seurat_create_seurat_object
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_seurat_tools'
- name: seurat_dim_plot
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_seurat_tools'
- name: seurat_export_cellbrowser
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_seurat_tools'
- name: seurat_filter_cells
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_seurat_tools'
- name: seurat_find_clusters
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_seurat_tools'
- name: seurat_find_markers
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_seurat_tools'
- name: seurat_find_variable_genes
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_seurat_tools'
- name: seurat_normalise_data
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_seurat_tools'
- name: seurat_read10x
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_seurat_tools'
- name: seurat_run_pca
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_seurat_tools'
- name: seurat_run_tsne
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_seurat_tools'
- name: seurat_scale_data
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_seurat_tools'
- name: seurat_find_neighbours
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_seurat_tools'
- name: monocle3_create
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_monocle3_tools'
- name: monocle3_diffexp
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_monocle3_tools'
- name: monocle3_learngraph
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_monocle3_tools'
- name: monocle3_ordercells
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_monocle3_tools'
- name: monocle3_partition
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_monocle3_tools'
- name: monocle3_plotcells
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_monocle3_tools'
- name: monocle3_preprocess
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_monocle3_tools'
- name: monocle3_reducedim
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_monocle3_tools'
- name: monocle3_topmarkers
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_monocle3_tools'
- name: run_sccaf
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_sccaf_tools'
- name: sccaf_asses
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_sccaf_tools'
- name: sccaf_asses_merger
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_sccaf_tools'
- name: sccaf_regress_out
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_sccaf_tools'
- name: scmap_preprocess_sce
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scmap_tools'
- name: scmap_index_cell
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scmap_tools'
- name: scmap_index_cluster
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scmap_tools'
- name: scmap_scmap_cell
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scmap_tools'
- name: scmap_scmap_cluster
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scmap_tools'
- name: scmap_select_features
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scmap_tools'
- name: scmap_get_std_output
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scmap_tools'
- name: ucsc_cell_browser
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_utils_viz'
- name: sceasy_convert
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_utils_viz'
- name: text_processing
owner: bgruening
tool_panel_section_label: 'Text Manipulation'
- name: umi_tools_count
owner: iuc
tool_panel_section_label: FASTA/FASTQ
- name: salmon_kallisto_mtx_to_10x
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_utils_viz'
- name: droplet_barcode_plot
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_utils_viz'
- name: ct_build_cell_ontology_dict
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_label_analysis_tools'
- name: ct_combine_tool_outputs
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_label_analysis_tools'
- name: ct_get_consensus_outputs
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_label_analysis_tools'
- name: ct_get_empirical_dist
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_label_analysis_tools'
- name: ct_get_tool_perf_table
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_label_analysis_tools'
- name: ct_get_tool_pvals
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_label_analysis_tools'
- name: garnett_check_markers
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_garnett_tools'
- name: garnett_classify_cells
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_garnett_tools'
- name: garnett_get_feature_genes
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_garnett_tools'
- name: garnett_get_std_output
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_garnett_tools'
- name: garnett_train_classifier
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_garnett_tools'
- name: garnett_transform_markers
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_garnett_tools'
- name: update_marker_file
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_garnett_tools'
- name: scpred_eigen_decompose
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scpred_tools'
- name: scpred_get_feature_space
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scpred_tools'
- name: scpred_get_std_output
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scpred_tools'
- name: scpred_preprocess_data
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scpred_tools'
- name: scpred_predict_labels
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scpred_tools'
- name: scpred_train_model
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scpred_tools'
- name: scpred_traint_test_split
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scpred_tools'
- name: scater_read_10x_results
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scater_tools'
- name: scater_normalize
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scater_tools'
- name: scater_is_outlier
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scater_tools'
- name: scater_filter
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scater_tools'
- name: scater_calculate_qc_metrics
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scater_tools'
- name: scater_calculate_cpm
owner: ebi-gxa
tool_panel_section_id: 'hca_sc_scater_tools'