arcinstitute/State-Parse-Filtered
The single cell RNA-seq dataset with human PBMC samples was sourced from Parse Biosciences [1]. [1] Performance of Evercode™ WT v3 in Human Immune Cells (PBMCs), https://www.parsebiosciences.com/datasets/performance-of-evercode-wt-v3-in-human-immune-cells-pbmcs/; Parse Biosciences, Seattle, USA; accessed 05/27/2025. Certain uses of this data may require a license from Parse Biosciences, Inc.
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1# Dataset paths - maps dataset names to their directories2[datasets]3parse = "/data/parse_final_concat"4 5# Training specifications6# All cell types in a dataset automatically go into training (excluding zeroshot/fewshot overrides)7[training]8parse = "train"9 10# Zeroshot specifications - entire cell types go to val or test11[zeroshot]12 13# Fewshot specifications - explicit perturbation lists14[fewshot]15[fewshot."parse.B_Naive"]16val = ['G-CSF', 'IFN-beta', 'M-CSF', 'IGF-1']17test = ['C5a', 'TWEAK', 'LIF', 'IL-17C', 'FGF-beta', 'BAFF', 'FLT3L', 'IFN-lambda2', '4-1BBL', 'IL-17E', 'IL-2', 'IL-19', 'PRL', 'IL-16', 'IL-7', 'GM-CSF', 'IL-17A', 'IL-13', 'IL-36-alpha', 'PSPN', 'EPO', 'IL-9', 'IL-31', 'IL-11', 'LT-alpha1-beta2', 'TL1A', 'IL-32-beta', 'IFN-omega', 'IL-8', 'Noggin', 'IFN-epsilon', 'IL-17F', 'Leptin', 'IL-33', 'IL-35', 'OSM', 'IL-34', 'HGF', 'IL-1Ra', 'LIGHT', 'CD27L', 'SCF', 'IL-1-alpha', 'TGF-beta1', 'CD30L', 'IL-24', 'IFN-gamma', 'IFN-alpha1', 'IFN-lambda1', 'GITRL', 'VEGF', 'ADSF', 'IL-15', 'EGF', 'IL-3', 'IL-17B', 'IL-6', 'IL-4', 'IL-10', 'CT-1', 'IFN-lambda3', 'TRAIL']18