[1-classifier.post-parturition]
FDR = 0.01

[1-classifier.pregnant]
FDR = 0.01

[2-cellSizeDistribution.post-parturition]
binStep = 200
minCellSize = 471

[2-cellSizeDistribution.pregnant]
binStep = 200
minCellSize = 4264

[3-mitochondrialContent.post-parturition]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0

[3-mitochondrialContent.pregnant]
method = absoluteThreshold
binStep = 0.3
maxFraction = 0

[4-numGenesVsNumUmis.post-parturition]
regressionType = linear
p.level = 0.0001038422

[4-numGenesVsNumUmis.pregnant]
regressionType = linear
p.level = 0.00002615063

[5-doubletScores.post-parturition]
binStep = 0.02
probabilityThreshold = 0.6091056

[5-doubletScores.pregnant]
binStep = 0.02
probabilityThreshold = 0.07280584

[6-dataIntegration.awsConfig]
region = eu-west-1

[6-dataIntegration.dataIntegration]
method = harmony
numGenes = 2000
normalisation = logNormalize

[6-dataIntegration.dimensionalityReduction]
method = rpca
numPCs = 30

[7-configureEmbedding.awsConfig]
region = eu-west-1

[7-configureEmbedding.embeddingSettings]
method = umap
distanceMetric = cosine
minimumDistance = 0.3

[7-configureEmbedding.clusteringSettings]
method = louvain
resolution = 0.8
