Closed RemyLau closed 8 months ago
Register existing transforms under their corresponding categories.
import dance.transforms for i in sorted(dance.registry.REGISTRY.children()): print(i)
Output:
dataset function function.genestats function.genestats.alpha function.genestats.cov_all function.genestats.fano_all function.genestats.max_all function.genestats.mean_all function.genestats.mu function.genestats.std_all function.metric preprocessor preprocessor.feature preprocessor.feature.cell preprocessor.feature.cell.BatchFeature preprocessor.feature.cell.CellPCA preprocessor.feature.cell.CellSVD preprocessor.feature.cell.SCNFeature preprocessor.feature.cell.WeightedFeaturePCA preprocessor.feature.gene preprocessor.feature.gene.GeneStats preprocessor.feature.spatial preprocessor.feature.spatial.MorphologyFeatureCNN preprocessor.feature.spatial.SMEFeature preprocessor.feature.spatial.SpatialIDEFeature preprocessor.filter preprocessor.filter.FilterScanpy preprocessor.filter.cell preprocessor.filter.cell.FilterCellsScanpy preprocessor.filter.gene preprocessor.filter.gene.FilterGenesCommon preprocessor.filter.gene.FilterGenesMarker preprocessor.filter.gene.FilterGenesMarkerGini preprocessor.filter.gene.FilterGenesMatch preprocessor.filter.gene.FilterGenesPercentile preprocessor.filter.gene.FilterGenesRegression preprocessor.filter.gene.FilterGenesScanpy preprocessor.filter.gene.FilterGenesTopK preprocessor.graph preprocessor.graph.cell preprocessor.graph.cell.CellFeatureBipartiteGraph preprocessor.graph.cell.CellFeatureGraph preprocessor.graph.cell.NeighborGraph preprocessor.graph.cell.PCACellFeatureGraph preprocessor.graph.cell.ScMoGNNGraph preprocessor.graph.feature preprocessor.graph.feature.FeatureFeatureGraph preprocessor.graph.reference preprocessor.graph.reference.DSTGraph preprocessor.graph.spatial preprocessor.graph.spatial.SMEGraph preprocessor.graph.spatial.SpaGCNGraph preprocessor.graph.spatial.SpaGCNGraph2D preprocessor.graph.spatial.StagateGraph preprocessor.interface preprocessor.interface.AnnDataTransform preprocessor.misc preprocessor.misc.Compose preprocessor.misc.RemoveSplit preprocessor.misc.SaveRaw preprocessor.misc.SetConfig preprocessor.normalize preprocessor.normalize.ScTransform preprocessor.normalize.ScaleFeature preprocessor.pseudobulk preprocessor.pseudobulk.CellGiottoTopicProfile preprocessor.pseudobulk.CellTopicProfile preprocessor.pseudobulk.PseudoMixture preprocessor.split preprocessor.split.entry preprocessor.split.entry.CellwiseMaskData preprocessor.split.entry.MaskData preprocessor.split.gene preprocessor.split.gene.GeneHoldout
A few recently implemented transforms have been marked as experimental and need further improvements in a future PR @xingzhongyu :
experimental
dance.transforms.spatial_feature.TangramFeature
dance.transforms.sc3_feature.SC3Feature
dance.transforms.pseudobulk.CellTypeNums
dance.transforms.graph.respet_graph.RESPETGraph
Things to improve:
obs
obsm
var
varm
uns
Register existing transforms under their corresponding categories.
Output:
TODOs
A few recently implemented transforms have been marked as
experimentaland need further improvements in a future PR @xingzhongyu :dance.transforms.spatial_feature.TangramFeaturedance.transforms.sc3_feature.SC3Featuredance.transforms.pseudobulk.CellTypeNumsdance.transforms.graph.respet_graph.RESPETGraphThings to improve:
obsorobsmfor cell level features, andvarorvarmfor gene level features. Prevent usage of wildcardunsif possible.