config.yaml

ROOT: /storage/groups/ml01/projects/2020_scIB_malte.luecken
r_env : scIB-R-integration
py_env : scIB-python
conv_env : scIB-R-conversion
timing: false

unintegrated_metrics: false

FEATURE_SELECTION:
  hvg: 2000
  full_feature: 0

SCALING:
  - unscaled
  - scaled

METHODS: # method name : ouput type(s)
  mnn: 
    output_type: full
  scanorama:
    output_type:
      - embed
      - full
  seurat:
    R: true
    output_type: full
  seuratrpca:
    R: true
    output_type: full
  saucie:
    output_type:
      - full
      - embed
  trvae:
    no_scale: true
    output_type: 
      - embed
      - full
  # trvaep:
  #   no_scale: true
  #   output_type:
  #     - embed
  #     - full
  harmony:
    R: true
    output_type: embed
  bbknn:
    output_type: knn
  scvi:
    no_scale: true
    output_type: embed
  conos:
    R: true
    output_type: knn
  combat:
    output_type: full
  liger:
    no_scale: true
    R: true
    output_type: embed
  scgen:
    output_type: full
    use_celltype: true
  scanvi:
    output_type: embed
    no_scale: true
    use_celltype: true
  fastmnn:
    R: true
    output_type:
      - embed
      - full
  desc:
    output_type: embed

DATA_SCENARIOS:
  pancreas:
    batch_key: tech
    label_key: celltype
    organism: human
    assay: expression
    file: /storage/groups/ml01/workspace/maren.buettner/data_integration/data/human_pancreas/human_pancreas_norm.h5ad
  lung_atlas:
    batch_key: batch
    label_key: cell_type
    organism: human
    assay: expression
    file: /storage/groups/ml01/workspace/group.daniela/lung/Lung_atlas_final_fixed.h5ad
  immune_cell_hum:
    batch_key: batch
    label_key: final_annotation
    organism: human
    assay: expression
    file: /storage/groups/ml01/workspace/group.daniela/immune_cells/Immune_ALL_human.h5ad
  immune_cell_hum_mou:
    batch_key: batch
    label_key: final_annotation
    organism: human
    assay: expression
    file: /storage/groups/ml01/workspace/group.daniela/immune_cells/Immune_ALL_hum_mou.h5ad
  simulations_1_1:
    batch_key: Batch
    label_key: Group
    organism: human
    assay: simulation
    file: /storage/groups/ml01/workspace/scIB/simulations_1_1/sim1_1_norm.h5ad
  simulations_2:
    batch_key: SubBatch
    label_key: Group
    organism: human
    assay: simulation
    file: /storage/groups/ml01/workspace/scIB/simulations_2/sim2_norm.h5ad

    #mouse_brain:
    #batch_key: study
    #label_key: cell_type
    #organism: mouse
    #assay: expression
    #file: /storage/groups/ml01/workspace/maren.buettner/data_integration/data/mouse_brain/mouse_brain_slim_cc_rev.h5ad
    #  mouse_brain_atac:
    #    batch_key: batchname
    #label_key: cell_type_consensus
    #organism: mouse
    #assay: atac
    #file: /mnt/znas/icb_zstore01/groups/ce01/workspace/Benchmarking_data_integration/data/brain_atac/atac_brain_processed.h5ad