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| tasks ingest ,,,,,,,,,,,,,,,,,, | ||
| Threads_high,Creating h5mu from filtered data files,Creating h5mu from bg data files, rna QC ,prot QC ,prot QC ,assess background,,,,,,,,,,,, | ||
| threads_medium,load_mudatas,load_bg_mudatas,downsample_bg_mudatas,run_scrublet,,,,,,,,,,,,,, | ||
| threads_low,run_repertoire_qc,run_atac_qc,plot_qc,10X metrics plotting,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| tasks preprocessed ,,,,,,,,,,,,,,,,,, | ||
| Threads_high,rna_preprocess,prot_preprocess,atac_preprocess,,,,,,,,,,,,,,, | ||
| threads_low,filter_mudata,postfilterplot,downsample,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| tasks integration ,,,,,,,,,,,,,,,,,, | ||
| Threads_high,run_no_batch_correct_rna,run_bbknn_rna,run_harmony_rna,run_combat_rna,run_scanorama_rna,run_scvi_rna,run_no_batch_correct_prot,run_harmony_prot,run_bbknn_prot,run_combat_prot,run_no_batch_correct_atac,run_harmony_atac,run_bbknn_atac,run_totalvi,run_multivi,run_mofa,run_wnn,merge_integration | ||
| threads_medium,Evaluation,plot_umaps,run_scib_metrics,,,,,,,,,,,,,,, | ||
| threads_low,run_lisi,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| tasks clustering ,,,,,,,,,,,,,,,,,, | ||
| Threads_high,run_neighbors,run_umap,find_markers,,,,,,,,,,,,,,, | ||
| threads_medium,run_clustering,collate_mdata,plot_cluster_umaps,plot_markers,,,,,,,,,,,,,, | ||
| threads_low,clustering,clustering,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| tasks vis ,,,,,,,,,,,,,,,,,, | ||
| Threads_high,plot_custom_markers_per_group,plot_custom_markers_umap,plot_categorical_umaps,write_obs,plot_scatters,,,,,,,,,,,,, | ||
| threads_low,plot_metrics,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| tasks refmap ,,,,,,,,,,,,,,,,,, | ||
| Threads_high,run_refmap_scvi,run_scib_refmap,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| tasks preprocessed spatial ,,,,,,,,,,,,,,,,,, | ||
| Threads_high,spatial_preprocess,,,,,,,,,,,,,,,,, | ||
| threads_low,filter_mudata,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| ,,,,,,,,,,,,,,,,,, | ||
| tasks spatial ,,,,,,,,,,,,,,,,,, | ||
| threads_medium,load_mudata,,,,,,,,,,,,,,,,, | ||
| threads_low,plotQC_spatial,,,,,,,,,,,,,,,,, | ||
| | **tasks ingest ** | | | | | | | | | | | | | | | | | | | | ||
| |------------------------------- |:--------------------------------------: |:--------------------------------: |:----------------------: |:--------------------: |:-----------------: |:-----------------: |--------------------------- |------------------ |---------------- |----------------- |--------------------------- |------------------ |---------------- |------------- |------------- |---------- |--------- |------------------- | | ||
| | Threads_high | Creating h5mu from filtered data files | Creating h5mu from bg data files | rna QC | prot QC | prot QC | assess background | | | | | | | | | | | | | | ||
| | threads_medium | load_mudatas | load_bg_mudatas | downsample_bg_mudatas | run_scrublet | | | | | | | | | | | | | | | | ||
| | threads_low | run_repertoire_qc | run_atac_qc | plot_qc | 10X metrics plotting | | | | | | | | | | | | | | | | ||
| | tasks preprocessed | | | | | | | | | | | | | | | | | | | | ||
| | Threads_high | rna_preprocess | prot_preprocess | atac_preprocess | | | | | | | | | | | | | | | | | ||
| | threads_low | filter_mudata | postfilterplot | downsample | | | | | | | | | | | | | | | | | ||
| | **tasks integration ** | | | | | | | | | | | | | | | | | | | | ||
| | Threads_high | run_no_batch_correct_rna | run_bbknn_rna | run_harmony_rna | run_combat_rna | run_scanorama_rna | run_scvi_rna | run_no_batch_correct_prot | run_harmony_prot | run_bbknn_prot | run_combat_prot | run_no_batch_correct_atac | run_harmony_atac | run_bbknn_atac | run_totalvi | run_multivi | run_mofa | run_wnn | merge_integration | | ||
| | threads_medium | Evaluation | plot_umaps | run_scib_metrics | | | | | | | | | | | | | | | | | ||
| | threads_low | run_lisi | | | | | | | | | | | | | | | | | | | ||
| | **tasks clustering ** | | | | | | | | | | | | | | | | | | | | ||
| | Threads_high | run_neighbors | run_umap | find_markers | | | | | | | | | | | | | | | | | ||
| | threads_medium | run_clustering | collate_mdata | plot_cluster_umaps | plot_markers | | | | | | | | | | | | | | | | ||
| | threads_low | clustering | clustering | | | | | | | | | | | | | | | | | | ||
| | **tasks vis ** | | | | | | | | | | | | | | | | | | | | ||
| | Threads_high | plot_custom_markers_per_group | plot_custom_markers_umap | plot_categorical_umaps | write_obs | plot_scatters | | | | | | | | | | | | | | | ||
| | threads_low | plot_metrics | | | | | | | | | | | | | | | | | | | ||
| | **tasks refmap ** | | | | | | | | | | | | | | | | | | | | ||
| | Threads_high | run_refmap_scvi | run_scib_refmap | | | | | | | | | | | | | | | | | | ||
| | tasks preprocessed spatial | | | | | | | | | | | | | | | | | | | | ||
| | Threads_high | spatial_preprocess | | | | | | | | | | | | | | | | | | | ||
| | threads_low | filter_mudata | | | | | | | | | | | | | | | | | | | ||
| | **tasks spatial ** | | | | | | | | | | | | | | | | | | | | ||
| | threads_medium | load_mudata | | | | | | | | | | | | | | | | | | | ||
| | threads_low | plotQC_spatial | | | | | | | | | | | | | | | | | | |