API

Import MultiVeloVAE as:

import multivelovae as vv

Preprocessing

aggregate_peaks_10x(adata_atac, ...[, ...])	Aggregate promoter and enhancer peaks to genes based on the 10X linkage file.
tfidf_norm(adata_atac[, scale_factor, copy])	Normalize counts in an AnnData object with TF-IDF.
knn_smooth_chrom(adata_atac[, nn_idx, ...])	Smooth (imputes) the count matrix with k nearest neighbors.
is_outlier(adata, metric[, lower_nmads, ...])	Find outlier cells via median absolute deviations.
regress_out(adata, keys[, layer, n_jobs, ...])	Regress out (mostly) unwanted sources of variation and optionally add intercept back.
filter_genes_dispersion(data[, flavor, ...])	Extract highly variable genes.

Velocity inference

VAEChrom(adata[, adata_atac, dim_z, ...])	MultiVeloVAE model for joint multi-omics velocity inference.
velocity(adata, adata_atac, key[, ...])	Compute multi-omic velocity for VAE.
velocity_graph(adata[, key, xkey, ...])	Normalize the velocity matrix and computes velocity graph with scvelo.tl.velocity_graph.

Differential test

differential_dynamics(adata, adata_atac, model)

Calculate differential dynamics between two groups of cells.

Plotting

dynamic_plot(adata, adata_atac, genes[, ...])	Gene dynamics plot.
scatter_plot(adata, adata_atac, genes[, ...])	Gene scatter plot.
velocity_embedding_stream(adata[, key, show])	Plot velocity streamplot with scvelo.pl.velocity_embedding_stream.
differential_dynamics_plot(adata, genes[, ...])	Plot differential dynamics between two groups of cells.
decoupling_plot(adata, genes[, group1, ...])	Plot decoupling or coupling dynamics between two groups of cells.