Roadmap

Development roadmap

flowchart LR
  classDef done fill:#a3f6cf,stroke:#000000;
  classDef wip fill:#f4cb93,stroke:#000000;
  classDef unprocessed fill:#afadff,stroke:#000000;

  Raw1[Sample 1] --> Split1[/Split\nmodalities/]:::done --> ProcGEX1 & ProcRNAV1 & ProcADT1 & ProcATAC1 & ProcVDJ1
  ProcGEX1[/Process GEX\nprofile/]:::done --> ConcatGEX[/Concatenate\nprofiles/]:::done --> ProcGEX[/Process GEX\nprofiles/]:::done
  ProcRNAV1[/Process RNAV\nprofile/]:::wip --> ConcatRNAV[/Concatenate\nprofiles/]:::done --> ProcRNAV[/Process RNAV\nprofiles/]:::wip
  ProcADT1[/Process ADT\nprofile/]:::done --> ConcatADT[/Concatenate\nprofiles/]:::done --> ProcADT[/Process ADT\nprofiles/]:::done
  ProcATAC1[/Process ATAC\nprofile/]:::unprocessed --> ConcatATAC[/Concatenate\nprofiles/]:::done --> ProcATAC[/Process ATAC\nprofiles/]:::unprocessed
  ProcVDJ1[/Process VDJ\nprofile/]:::unprocessed --> ConcatVDJ[/Concatenate\nprofiles/]:::done --> ProcVDJ[/Process VDJ\nprofiles/]:::unprocessed
  ProcGEX & ProcRNAV & ProcADT & ProcATAC & ProcVDJ --> Merge[/Merge\nmodalities/]:::done --> SetupIntegration[/Setup\nintegration/]:::done --> Integration[/Integration/]:::done

Figure 1: Status of implemented components. Green: implemented, orange: work in progress, purple: modality included in output but unprocessed,
GEX: Gene-expression. RNAV: RNA Velocity. ADT: Antibody-Derived Tags. ATAC: Assay for Transposase-Accessible Chromatin.

flowchart TB
  subgraph ingestion
    direction TB
    subgraph cellranger_multi
      direction TB
      mapping_10x --> convert_to_h5mu_10x
      mapping_10x[mapping]:::done
      convert_to_h5mu_10x[convert_to_h5mu]:::done
    end
    subgraph bdrhap_v1
      direction TB
      mapping_bd1 --> convert_to_h5mu_bd1
      mapping_bd1[mapping]:::done
      convert_to_h5mu_bd1[convert_to_h5mu]:::done
    end
    subgraph bdrhap_v2
      direction TB
      mapping_bd2 --> convert_to_h5mu_bd2
      mapping_bd2[mapping]:::wip
      convert_to_h5mu_bd2[convert_to_h5mu]:::wip
    end
    cellranger_multi:::subwf
    bdrhap_v1:::subwf
    bdrhap_v2:::subwf
  end
  ingestion:::wf
  subgraph process_samples
    split_modalities --> rna_singlesample & prot_singlesample & gdo_singlesample & atac_singlesample & other_modalities --> concat --> process_batches
    split_modalities:::done
    rna_singlesample:::done
    prot_singlesample:::done
    gdo_singlesample:::done
    atac_singlesample:::todo
    other_modalities:::done
    concat:::done
    subgraph process_batches
      direction LR
      split_modalities2 --> rna_multisample & prot_multisample & atac_multisample & other_modalities2 --> merge
      split_modalities2[split_modalities]:::done
      other_modalities2[other_modalities]:::done
      rna_multisample:::done
      prot_multisample:::done
      merge:::done
    end
    process_batches:::subwf
    atac_multisample:::todo
  end
  process_samples:::wf
  raw_counts --- ingestion --> raw_h5mu
  raw_h5mu --- process_samples --> processed_h5mu
  subgraph integration
    direction LR
    integration_method --> find_neighbors --> leiden --> umap
    integration_method -.- intmeth
    integration_method:::done
    find_neighbors:::done
    leiden:::done
    umap:::done
    subgraph intmeth [integration_method]
      bbknn:::done
      harmony:::done
      scanorama:::done
      scvi:::done
      totalvi:::done
      scgpt_integration:::wip
    end
    intmeth:::info
  end
  integration:::wf
  processed_h5mu --- integration ---> integrated_h5mu
  subgraph celltype_annotation
    direction TB
    integration_method2[integration_method]:::done
    celltypist:::wip
    scanvi:::wip
    scgpt_annotation:::wip
    onclass:::todo
    svm:::todo
    randomforest:::todo
    pynndescent_knn:::wip
    consensus_voting:::todo
    integration_method2 --> pynndescent_knn --> consensus_voting
    celltypist & scanvi & scgpt_annotation & onclass & svm & randomforest --> consensus_voting
  end
  reference_atlas --> celltype_annotation
  celltype_annotation:::wf
  integrated_h5mu --- celltype_annotation --> annotated_h5mu

  classDef done fill:#ccebc5,stroke:#4daf4a
  classDef wip fill:#fed9a6,stroke:#ff7f00
  classDef todo fill:#fbb4ae,stroke:#e41a1c
  classDef wf fill:#f0f0f0,stroke:#525252
  classDef subwf fill:#d9d9d9,stroke:#525252
  classDef info fill:#f0f0f0,stroke:#525252,stroke-dasharray: 4 4
  
  subgraph Legend
    done[Done]:::done
    wip[Work in progress]:::wip
    todo[To do]:::todo
  end
  Legend:::info

Figure 2