API
Import SCALEX:
import scalex
Function
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Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space |
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Label transfer |
Data
Load data
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Load dataset with preprocessing |
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Concatenate multiple datasets along the observations axis with name |
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Load single cell dataset from files |
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Load single cell dataset from file |
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Read mtx format data folder including: |
Preprocessing
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Preprocessing single-cell data |
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Preprocessing single-cell RNA-seq data |
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Preprocessing single-cell ATAC-seq |
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Batch-specific scale data |
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Reindex AnnData with gene list |
DataLoader
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Dataloader of single-cell data |
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Batch-specific Sampler sampled data of each batch is from the same dataset. |
Net
Model
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VAE framework |
Layer
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Domain-specific Batch Normalization |
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Basic block consist of: |
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Neural network consist of multi Blocks |
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VAE Encoder |
Loss
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Utils
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Make the input tensor one hot tensors |
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Early stops the training if loss doesn't improve after a given patience. |
Plot
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plot separated embeddings with others as background |
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Plot meta correlations among batches |
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Plot meta correlations between two batches |
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Plot confusion matrix |
Metric
Collections of useful measurements for evaluating results.
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Calculate batch entropy mixing score |
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Compute the mean Silhouette Coefficient of all samples. |
Logger
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