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config.yaml
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n_jobs: 8 # Threads
names: ['parse', '10x']
count_adata:
parse:
/Users/nargesrezaie/Documents/MortazaviLab/Topyfic/workflow/snakemake/resources/Bridge_LeftCortex_Parse_harmony_annotated_Topyfic_regGene.h5ad
10x:
/Users/nargesrezaie/Documents/MortazaviLab/Topyfic/workflow/snakemake/resources/Bridge_LeftCortex_10x_harmony_annotated_Topyfic_regGene.h5ad
n_topics: [5, 10] #, 15, 20, 25, 30, 35, 40, 45, 50]
organism: mouse # human or mouse
workdir: /Users/nargesrezaie/Documents/MortazaviLab/Topyfic/workflow/snakemake/results/
train:
n_runs: 100
random_states: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21, 22, 23, 24, 25, 26, 27, 28, 29,
30, 31, 32, 33, 34, 35, 36, 37, 38, 39,
40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
50, 51, 52, 53, 54, 55, 56, 57, 58, 59,
60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
70, 71, 72, 73, 74, 75, 76, 77, 78, 79,
80, 81, 82, 83, 84, 85, 86, 87, 88, 89,
90, 91, 92, 93, 94, 95, 96, 97, 98, 99]
top_model:
n_top_genes: None
resolution: 1
max_iter_harmony: 10
min_cell_participation: None
merge: True