config.yaml

seed: 12345
external_dir: "data/external/"
interim_dir: "data/interim/"
processed_dir: "data/processed/"
raw_dir: "data/raw/"
fl_cores: ["FLcoreNoPseudorep", "FLcoreSC", "FLcorePseudotech"]
samples: ["FL", "yBM"]
donors: ["yBM1", "yBM2", "FL1", "FL2"]
deseq_cutoffs:
  log2foldchange: 1
  adjustedpvalue: 0.05
seurat_deg_cutoffs:
  log2foldchange:
    main: 0.5
    extra: [0.25, 1.0]
    all: [0.25, 0.5, 1.0]
  adjustedpvalue: 0.05
random_params:
  iterations: 10000
fl_clusters_to_use:
  ["Cyc", "DC.Mono", "GMP", "HSC", "Ly.I", "Ly.II", "MEP", "MPP.I", "MPP.II"]
gates_to_use:
  [
    "CD7_CLP",
    "CD10_CLP",
    "CD38neg_MPP",
    "CD49Fpos_HSC",
    "CD90pos_HSC",
    "CMP_123",
    "CMP_135",
    "GMP_123",
    "GMP_135",
    "IL7RA_CLP",
    "LMPP",
    "MEP_123",
    "MEP_135",
  ]
leukemia_types:
  [
    "KMT2A-MLLT1",
    "BCR-ABL1",
    "KMT2A-AFF1",
    "High hyperdiploid",
    "Low hyperdiploid",
    "ETV6-RUNX1",
    "KMT2A-MLLT3",
  ]