/
integration-config-all.json
76 lines (76 loc) · 2.24 KB
/
integration-config-all.json
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{
"global_default" :{
"covariate" : ["batch"],
"combination" : ["Mus_musculus_Macaca_fascicularis_Homo_sapiens"]
},
"TabulaDroplet":{
"default": {
"transform" : ["libSize","sqrt","scran", "standard"],
"method" : ["CCA", "bbknn","insct", "magic", "scanorama", "harmony", "fastMNN", "combat", "none"],
"n_features" : [2000],
"add_intron" : ["N"],
"dims" : [8, 30],
"knn" : [7],
"dist" : [0.3],
"neighbors" : [30]
},
"scVI" : {
"transform" : ["counts"],
"add_intron": ["Y", "N"],
"n_features" : [1000, 2000, 5000, 10000],
"dims" : [4,6,8,10,20,30,50,100],
"knn" : [0.8,0.4,0.6,5, 7, 10],
"dist": [0.1],
"neighbors": [500]
},
"scArches":{
"transform" : ["counts"],
"dist" : [0.3],
"neighbors" : [30]
}
},
"onlyWELL":{
"default": {
"transform" : ["libSize","sqrt","scran", "standard"],
"method" : ["bbknn","insct","magic", "scanorama", "harmony", "fastMNN", "combat", "none"],
"add_intron" : ["N"],
"n_features" : [500, 1000, 2000],
"covariate" : ["batch"],
"dims" : [4, 8, 30],
"dist" : [0.1],
"knn" : [7],
"neighbors": [30]
},
"scVI": {
"transform" : ["counts"]
},
"CCA":{
"transform" :["SCT"]
}
},
"universe":{
"default": {
"transform" : ["counts"],
"method" : ["scVI"],
"add_intron" : ["N"],
"n_features" : [2000, 5000, 10000],
"dims" : [30,50,100],
"knn": [7],
"dist" : [0.1],
"neighbors" : [100]
}
},
"celltype_subset":{
"default": {
"transform" : ["counts"],
"method" : ["scVI"],
"add_intron": ["N"],
"partition" : ["cones", "hc", "rgc", "amacrine", "mullerglia", "bipolar", "rods"],
"n_features" : [ 1000, 2000],
"dims" : [4,6,10,30],
"knn" : [7, 10, 15],
"dist" : [0.1],
"neighbors" : [30]
}
}
}