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config.default.yml
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config.default.yml
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#--- PREPROCESS ------
output_dir_benchmark: ""
#--- CONSENSUS -------
consensus:
tools:
- 'all'
type:
majority:
min_agree: [0]
CAWPE:
alpha: [0]
mode: ""
accuracy_metric: "F1"
#--- NOTEBOOKS -------
# genes of interest
# space separated string: "PDGFRA MOG GFAP RBFOX1"
marker_genes: ""
#--- BENCHMARK -------
benchmark:
n_folds: 5
#---- TOOLS ----------
SingleR:
threads: 1
Correlation:
threads: 1
scPred:
threads: 1
classifier: 'svmRadial'
scClassify:
threads: 1
topN: 50
weightsCal: False
hopach_kmax: 5
algorithm: "WKNN"
similarity: "pearson"
prob_threshold: 0.7
cor_threshold_static: 0.5
cor_threshold_high: 0.7
SciBet:
threads: 1
singleCellNet:
threads: 1
nTrees: 500
scHPL:
threads: 1
classifier: 'svm'
dimred: 'False'
threshold: 0.5
SVMlinear:
threads: 1
threshold: 0
classifier: 'SVMlinear'
SVC:
threads: 1
classifier: 'rbf'
threshold: 0.5
ACTINN:
threads: 1
scLearn:
threads: 1
bootstrap_times: 10
scID:
threads: 1
estimate_weights_from_target: False
logFC: 0.5
scAnnotate:
threads: 1
threshold: 0.5
scNym:
threads: 1
threshold: 0.5
CellTypist:
threads: 1
feature_selection: 'True'
majority_voting: 'True'
threshold: 0.5
Seurat:
threads: 1
nPC_computed: 50
nPC_used: 30
integration_method: 'CCAIntegration'
scANVI:
threshold: 0.5
Symphony:
threads: 1
nPC_computed: 50
CellBlast:
threads: 1
threshold: 0.5
n_models: 4
#-----------------