Mapping Vector Field of Single Cells

API

Import dynamo as:

import dynamo as dyn

Data IO

(See more at anndata-docs)

read(filename[, backed, as_sparse, ...])	Read .h5ad-formatted hdf5 file.
read_h5ad(filename[, backed, as_sparse, ...])	Read .h5ad-formatted hdf5 file.
read_loom(filename, *[, sparse, cleanup, ...])	Read .loom-formatted hdf5 file.

Preprocessing (pp)

pp.convert2symbol(adata[, scopes, subset])	This helper function converts unofficial gene names to official gene names.
pp.filter_cells(adata[, filter_bool, layer, ...])	Select valid cells based on a collection of filters including spliced, unspliced and protein min/max vals.
pp.filter_cells_by_outliers(adata[, ...])	Select valid cells based on a collection of filters including spliced, unspliced and protein min/max vals.
pp.filter_genes(adata[, filter_bool, layer, ...])	Basic filter of genes based a collection of expression filters.
pp.filter_genes_by_pattern(adata[, ...])	Utility function to filter mitochondria, ribsome protein and ERCC spike-in genes, etc.
pp.filter_genes_by_outliers(adata[, ...])	Basic filter of genes based a collection of expression filters.
pp.filter_genes_by_clusters(adata, cluster)	Prepare filtering genes on the basis of cluster-wise expression threshold.
pp.calc_sz_factor(adata_ori[, layers, ...])	Calculate the size factor of each cell using geometric mean or median of total UMI across cells for a AnnData object.
pp.normalize(adata[, layers, ...])	Normalize the gene expression value for the AnnData object.
pp.normalize_cells(adata[, layers, ...])	Normalize the gene expression value for the AnnData object.
pp.normalize_layers_pearson_residuals(adata)	Normalize the given layers of the AnnData object using Pearson residuals.
pp.calc_Gini(adata[, layers])	Calculate the Gini coefficient of a numpy array.
pp.select_genes_monocle(adata[, layer, ...])	Select genes based on monocle recipe.
pp.select_genes_by_pearson_residuals(adata)	Gene selection and normalization based on [Lause21].
pp.scale(adata[, layers, scale_to_layer, ...])	Scale layers to a particular total expression value, similar to normalize_expr_data function.
pp.log1p(adata[, layers, copy])	Perform log1p transform on selected adata layers
pp.pca(adata[, X_data, n_pca_components, ...])	Perform PCA reduction for monocle recipe.
pp.top_pca_genes(adata[, pc_key, ...])	Define top genes as any gene that is n_top_genes in some principle component.
pp.sctransform(adata[, layers, ...])	A wrapper calls sctransform_core and set dynamo style keys in adata
pp.Preprocessor([...])	Preprocessor constructor.
pp.CnmfPreprocessor(**kwargs)	A specialized preprocessor based on cNMF.
pp.harmony_debatch(adata, key[, basis, ...])	Use harmonypy [Korunsky19] to remove batch effects.
pp.integrate(adatas[, batch_key, fill_value])	Concatenating all anndata objects.
pp.lambda_correction(adata[, lambda_key, ...])	Use lambda (cell-wise detection rate) to estimate the labelled RNA.
pp.decode(adata)	Decode an AnnData object.
pp.cell_cycle_scores(adata[, layer, ...])	Estimate cell cycle stage of each cell based on its gene expression pattern.

Estimation (est)

Note

Classes in est are internally to Tools. See our estimation classes here: estimation

Tools (tl)

kNN and moments of expressions

tl.neighbors(adata[, X_data, genes, basis, ...])	Search nearest neighbors of the adata object.
tl.mnn(adata[, n_pca_components, ...])	Calculate mutual nearest neighbor graph across specific data layers.
tl.moments(adata[, X_data, genes, group, ...])	Calculate kNN based first and second moments (including uncentered covariance) for different layers of data.

Kinetic parameters and RNA/protein velocity

tl.dynamics(adata[, filter_gene_mode, ...])

Inclusive model of expression dynamics considers splicing, metabolic labeling and protein translation.

Labeling Velocity recipes

tl.recipe_deg_data(adata[, tkey, reset_X, ...])	An analysis recipe that properly pre-processes different layers for a degradation experiment with both labeling and splicing data or only labeling.
tl.recipe_kin_data(adata[, tkey, reset_X, ...])	An analysis recipe that properly pre-processes different layers for an kinetics experiment with both labeling and splicing or only labeling data.
tl.recipe_mix_kin_deg_data(adata[, tkey, ...])	An analysis recipe that properly pre-processes different layers for a mixture kinetics and degradation experiment with both labeling and splicing or only labeling data.
tl.recipe_one_shot_data(adata[, tkey, ...])	An analysis recipe that properly pre-processes different layers for a one-shot experiment with both labeling and splicing data.
tl.velocity_N(adata[, group, ...])	Use new RNA based pca, umap, for velocity calculation and projection for kinetics or one-shot experiment.

Dimension reduction

tl.reduceDimension(adata[, X_data, genes, ...])	Compute a low dimension reduction projection of an AnnData object first with PCA, followed by non-linear dimension reduction methods
tl.DDRTree(X, maxIter, sigma, gamma[, eps, ...])	Provides an implementation of the framework of reversed graph embedding (RGE).
tl.psl(Y[, sG, dist, K, C, param_gamma, d, ...])	This function is a pure Python implementation of the PSL algorithm.

Clustering

tl.hdbscan(adata[, X_data, genes, layer, ...])	Apply hdbscan to cluster cells in the space defined by basis.
tl.infomap(adata[, use_weight, adj_matrix, ...])	Apply infomap community detection algorithm to cluster adata.
tl.leiden(adata[, resolution, use_weight, ...])	Apply leiden clustering to the input adata.
tl.louvain(adata[, resolution, use_weight, ...])	Apply louvain clustering to adata.
tl.scc(adata[, min_cells, spatial_key, ...])	Spatially constrained clustering (scc) to identify continuous tissue domains.

Velocity projection

tl.cell_velocities(adata[, ekey, vkey, X, ...])	Project high dimensional velocity vectors onto given low dimensional embeddings, and/or compute cell transition
tl.confident_cell_velocities(adata, group, ...)	Compute transition probability and perform velocity projection

Velocity metrics

tl.cell_wise_confidence(adata[, X_data, ...])	Calculate the cell-wise velocity confidence metric.
tl.gene_wise_confidence(adata, group[, ...])	Diagnostic measure to identify genes contributed to "wrong" directionality of the vector flow.

Markov chain

tl.generalized_diffusion_map(adata, **kwargs)	Apply the diffusion map algorithm on the transition matrix build from Itô kernel.
tl.stationary_distribution(adata[, method, ...])	Compute stationary distribution of cells using the transition matrix.
tl.diffusion(M[, P0, steps, backward])	Find the state distribution of a Markov process.
tl.expected_return_time(M[, backward])	Find the expected returning time.

Markers and differential expressions

tl.moran_i(adata[, X_data, genes, layer, ...])	Identify genes with strong spatial autocorrelation with Moran's I test.
tl.find_group_markers(adata, group[, genes, ...])	Find marker genes for each group of cells based on gene expression or velocity values as specified by the layer.
tl.two_groups_degs(adata[, genes, layer, ...])	Find marker genes between two groups of cells based on gene expression or velocity as specified by the layer.
tl.top_n_markers(adata[, with_moran_i, ...])	Filter cluster deg (Moran's I test) results and retrieve top markers for each cluster.
tl.glm_degs(adata[, X_data, genes, layer, ...])	Differential genes expression tests using generalized linear regressions.

Cell proliferation and apoptosis

tl.score_cells(adata[, genes, layer, basis, ...])	Score cells based on a set of genes.
tl.cell_growth_rate(adata, group, source, target)	Estimate the growth rate via clone information or logistic equation of population dynamics.

*Converter and helper *

tl.converter(data_in[, from_type, to_type, dir])	Convert adata to loom object or vice versa.
tl.run_scvelo(adata)	Run Scvelo over the AnnData.
tl.run_velocyto(adata)	Run velocyto over the AnnData object.
tl.vlm_to_adata(vlm[, n_comps, basis, ...])	Conversion function from the velocyto world to the dynamo world.

Vector field (vf)

Vector field reconstruction

Note

Vector field class is internally to vf.VectorField. See our vector field classes here: vector field

vf.VectorField(adata[, basis, layer, dims, ...])	Learn a function of high dimensional vector field from sparse single cell samples in the entire space robustly.
vf.SparseVFC(X, Y, Grid[, M, a, beta, ecr, ...])	Apply sparseVFC (vector field consensus) algorithm to learn a functional form of the vector field from random samples with outlier on the entire space robustly and efficiently.
vf.BaseVectorField([X, V, Grid])	The BaseVectorField class is a base class for storing and manipulating vector fields.
vf.SvcVectorField([X, V, Grid])	Initialize the VectorField class.
vf.graphize_vecfld(*args, **kw)
vf.vector_field_function(*args, **kw)

Vector field topology

vf.cluster_field(adata[, basis, features, ...])	Cluster cells based on vector field features.
vf.topography(adata[, basis, layer, X, ...])	Map the topography of the single cell vector field in (first) two dimensions.
vf.FixedPoints([X, J])	The FixedPoints class stores a list of fixed points and their corresponding Jacobian matrices, and provides methods for computing the eigenvalues of the Jacobian matrices, determining the stability of the fixed points, and identifying saddle/stable fixed points.
vf.VectorField2D(func[, func_vx, func_vy, ...])	The VectorField2D class is a class that represents a 2D vector field, which is a type of mathematical object that assigns a 2D vector to each point in a 2D space.
vf.assign_fixedpoints(adata[, basis, cores, ...])	Assign each cell in our data to a fixed point.

Beyond RNA velocity

vf.velocities(adata[, init_cells, ...])	Calculate the velocities for any cell state with the reconstructed vector field function.
vf.speed(adata[, basis, vector_field_class, ...])	Calculate the speed for each cell with the reconstructed vector field function.
vf.jacobian(adata[, regulators, effectors, ...])	Calculate Jacobian for each cell with the reconstructed vector field.
vf.divergence(adata[, cell_idx, sampling, ...])	Calculate divergence for each cell with the reconstructed vector field function.
vf.curl(adata[, basis, vector_field_class, ...])	Calculate Curl for each cell with the reconstructed vector field function.
vf.acceleration(adata[, basis, ...])	Calculate acceleration for each cell with the reconstructed vector field function.
vf.curvature(adata[, basis, ...])	Calculate curvature for each cell with the reconstructed vector field function.
vf.torsion(adata[, basis, vector_field_class])	Calculate torsion for each cell with the reconstructed vector field function.
vf.sensitivity(adata[, regulators, ...])	Calculate Sensitivity matrix for each cell with the reconstructed vector field.

Beyond velocity vector field

vf.cell_accelerations(adata[, vf_basis, ...])	Compute RNA acceleration field via reconstructed vector field and project it to low dimensional embeddings.
vf.cell_curvatures(adata[, vf_basis, basis, ...])	Compute RNA curvature field via reconstructed vector field and project it to low dimensional embeddings.

Vector field ranking

vf.rank_cells(adata, arr_key[, groups, ...])	Rank cell's absolute, positive, negative vector field metrics by different gene groups.
vf.rank_genes(adata, arr_key[, groups, ...])	Rank gene's absolute, positive, negative vector field metrics by different cell groups.
vf.rank_expression_genes(adata[, ekey, ...])	Rank genes based on their expression values for each cell group.
vf.rank_velocity_genes(adata[, vkey, ...])	Rank genes based on their raw and absolute velocities for each cell group.
vf.rank_divergence_genes(adata[, jkey, ...])	Rank genes based on their diagonal Jacobian for each cell group.
vf.rank_acceleration_genes(adata[, akey, ...])	Rank genes based on their absolute, positive, negative accelerations for each cell group.
vf.rank_curvature_genes(adata[, ckey, ...])	Rank gene's absolute, positive, negative curvature by different cell groups.
vf.rank_jacobian_genes(adata[, groups, ...])	Rank genes or gene-gene interactions based on their Jacobian elements for each cell group.
vf.rank_s_divergence_genes(adata[, skey, ...])	Rank genes based on their diagonal Sensitivity for each cell group.
vf.rank_sensitivity_genes(adata[, groups, ...])	Rank genes or gene-gene interactions based on their sensitivity elements for each cell group.

Single cell potential: three approaches

vf.gen_fixed_points(func, auto_func, ...[, ...])	Calculate the fixed points of (learned) vector field function .
vf.gen_gradient(dim, N, Function, ...)	Calculate the gradient of the (learned) vector field function for the least action path (LAP) symbolically
vf.IntGrad(points, Function, DiffusionMatrix, dt)	Calculate the action of the path based on the (reconstructed) vector field function and diffusion matrix (Eq.
vf.DiffusionMatrix(x)	Diffusion matrix can be variable dependent
vf.action(n_points, tmax, point_start, ...)	It calculates the minimized action value given an initial path, ODE, and diffusion matrix.
vf.Potential(adata[, DiffMat, method])	Function to map out the pseudo-potential landscape.
vf.path_integral(VecFnc, x_lim, y_lim, ...)	A deterministic map of Waddington’s epigenetic landscape for cell fate specification Sudin Bhattacharya, Qiang Zhang and Melvin E.
vf.alignment(numPaths, numTimeSteps, ...[, ...])	Align potential values so all path-potentials end up at same global min and then generate potential surface with interpolation on a grid.
vf.Wang_action(X_input, F, D, dim, N[, lamada_])	Calculate action by path integral by Wang's method.
vf.Wang_LAP(F, n_points, point_start, point_end)	Calculating least action path based methods from Jin Wang and colleagues (http://www.pnas.org/cgi/doi/10.1073/pnas.1017017108)
vf.transition_rate(X_input, F[, D, lambda_])	Calculate the rate to convert from one cell state to another cell state by taking the optimal path.
vf.MFPT(X_input, F[, D, lambda_])	Calculate the MFPT (mean first passage time) to convert from one cell state to another cell state by taking the optimal path.
vf.Ao_pot_map(vecFunc, X[, fjac, D])	Mapping potential landscape with the algorithm developed by Ao method. References: Potential in stochastic differential equations: novel construction. Journal of physics A: mathematical and general, Ao Ping, 2004.
vf.solveQ(*args, **kw)

Stochastic processes

vf.diffusionMatrix(adata[, X_data, V_data, ...])

Calculate the diffusion matrix from the estimated velocity vector and the reconstructed vector field.

Vector field clustering and graph

vf.cluster_field(adata[, basis, features, ...])	Cluster cells based on vector field features.
vf.streamline_clusters(adata[, basis, ...])	Cluster 2D streamlines based on vector field features.
vf.vfGraph(*args, **kwds)	A class for manipulating the graph creating from the transition matrix, built from the (reconstructed) vector field.

Prediction (pd)

pd.andecestor(adata, init_cells[, ...])	Predict the ancestors or descendants of a group of initial cells (states) with the given vector field function.
pd.fate(adata, init_cells[, init_states, ...])	Predict the historical and future cell transcriptomic states over arbitrary time scales.
pd.fate_bias(adata, group[, basis, inds, ...])	Calculate the lineage (fate) bias of states whose trajectory are predicted.
pd.get_init_path(G, start, end, coords[, ...])
pd.least_action(adata, init_cells, target_cells)	Calculate the optimal paths between any two cell states.
pd.perturbation(adata, genes[, expression, ...])	In silico perturbation of single-cells and prediction of cell fate after perturbation.
pd.state_graph(adata, group[, method, ...])	Estimate the transition probability between cell types using method of vector field integrations or Markov chain lumping.
pd.KO(adata, KO_genes[, vecfld, vf_key, ...])	In silico knockout genes (and thus the vector field function) and prediction of cell fate after knockout.
pd.rank_perturbation_cell_clusters(adata[, ...])	Rank cells based on their raw and absolute perturbation for each cell group.
pd.rank_perturbation_cells(adata[, pkey, ...])	Rank cells based on their raw and absolute perturbation for each cell group.
pd.rank_perturbation_genes(adata[, pkey, ...])	Rank genes based on their raw and absolute perturbation effects for each cell group.
pd.state_graph(adata, group[, method, ...])	Estimate the transition probability between cell types using method of vector field integrations or Markov chain lumping.
pd.tree_model(adata, group, progenitor, ...)	This function learns a tree model of cell states (types).

Plotting (pl)

Preprocessing

pl.basic_stats(adata[, group, figsize, ...])	Plot the basic statics (nGenes, nCounts and pMito) of each category of adata.
pl.show_fraction(adata[, genes, group, ...])	Plot the fraction of each category of data used in the velocity estimation.
pl.feature_genes(adata[, layer, mode, ...])	Plot selected feature genes on top of the mean vs.
pl.biplot(adata[, pca_components, pca_key, ...])	A biplot overlays a score plot and a loadings plot in a single graph.
pl.loading(adata[, n_pcs, loading_key, ...])	Plot the top absolute pca loading genes.
pl.variance_explained(adata[, threshold, ...])	Plot the accumulative variance explained by the principal components.
pl.highest_frac_genes(adata[, n_top, ...])	Plot the top genes.
pl.exp_by_groups(adata, genes[, layer, ...])	Plot the (labeled) expression values of genes across different groups (time points).
pl.bubble(adata, genes, group[, gene_order, ...])	Bubble plots generalized to velocity, acceleration, curvature.

Cell cycle staging

pl.cell_cycle_scores(adata[, cells, ...])

Plot a heatmap of cells ordered by cell cycle position.

Scatter base

pl.scatters(adata[, basis, x, y, z, color, ...])

Plot an embedding as points.

Space plot

pl.space(adata[, color, genes, gene_cmaps, ...])

Scatter plot for physical coordinates of each cell.

Phase diagram: conventional scRNA-seq

pl.phase_portraits(adata, genes[, x, y, ...])

Draw the phase portrait, expression values, velocity on the low dimensional embedding.

Kinetic models: labeling based scRNA-seq

pl.dynamics(adata, genes[, unit, ...])

Plot the data and fitting of different metabolic labeling experiments.

Kinetics

pl.kinetic_curves(adata, genes[, mode, ...])	Plot the gene expression dynamics over time (pseudotime or inferred real time) as kinetic curves.
pl.kinetic_heatmap(adata, genes[, mode, ...])	Plot the gene expression dynamics over time (pseudotime or inferred real time) in a heatmap.
pl.jacobian_kinetics(adata[, basis, ...])	Plot the Jacobian dynamics over time (pseudotime or inferred real time) in a heatmap.
pl.sensitivity_kinetics(adata[, basis, ...])	Plot the Sensitivity dynamics over time (pseudotime or inferred real time) in a heatmap.

Dimension reduction

pl.pca(adata, *args, **kwargs)	Scatter plot with pca basis.
pl.tsne(adata, *args, **kwargs)	Scatter plot with tsne basis.
pl.umap(adata, *args, **kwargs)	Scatter plot with umap basis.
pl.trimap(adata, *args, **kwargs)	Scatter plot with trimap basis.

Clustering

pl.leiden(adata[, basis, color])	Scatter plot for leiden community detection in selected basis.
pl.louvain(adata[, basis, color, color_key_cmap])	Scatter plot for louvain community detection in selected basis.
pl.infomap(adata[, basis, color])	Scatter plot for infomap community detection in selected basis.
pl.streamline_clusters(adata[, basis, ...])	Scatter plot for visualizing streamline clusters in selected basis.

Neighbor graph

pl.nneighbors(adata[, x, y, color, basis, ...])	Plot nearest neighbor graph of cells used to embed data into low dimension space.
pl.state_graph(adata[, group, ...])	Plot a summarized cell type (state) transition graph.

Vector field plots: velocities and accelerations

pl.cell_wise_vectors(adata[, basis, x, y, ...])	Plot the velocity or acceleration vector of each cell.
pl.cell_wise_vectors_3d(adata[, basis, x, ...])	Plot the velocity or acceleration vector of each cell.
pl.grid_vectors(adata[, basis, x, y, ekey, ...])	Plot the velocity or acceleration vector of each cell on a grid.
pl.streamline_plot(adata[, basis, x, y, ...])	Plot the velocity vector of each cell.
pl.line_integral_conv(adata[, basis, ...])	Visualize vector field with quiver, streamline and line integral convolution (LIC), using velocity estimates on a
pl.plot_energy(adata[, basis, vecfld_dict, ...])	Plot the energy and energy change rate over each optimization iteration.
pl.plot_3d_streamtube(adata, color, layer, ...)	Plot a interative 3d streamtube plot via plotly.

Vector field topology

pl.plot_flow_field(vecfld, x_range, y_range)	Plots the flow field with line thickness proportional to speed.
pl.plot_fixed_points(vecfld[, vecfld_dict, ...])	Plot fixed points stored in the VectorField2D class.
pl.plot_fixed_points_2d(vecfld[, marker, ...])	Plot fixed points stored in the VectorField2D class.
pl.plot_nullclines(vecfld[, vecfld_dict, ...])	Plot nullclines stored in the VectorField2D class.
pl.plot_separatrix(vecfld, x_range, y_range, t)	Plot separatrix on phase portrait.
pl.plot_traj(f, y0, t[, args, lw, ...])	Plots a trajectory on a phase portrait.
pl.topography(adata[, basis, fps_basis, x, ...])	Plot the streamline, fixed points (attractor / saddles), nullcline, separatrices of a recovered dynamic system for single cells.
pl.response(adata, pairs_mat[, xkey, ykey, ...])	Plot the lagged DREVI plot pairs of genes across pseudotime.

Beyond RNA velocity

pl.speed(adata[, basis, color, frontier])	Scatter plot with cells colored by the estimated velocity speed (and other information if provided).
pl.divergence(adata[, basis, color, cmap, ...])	Scatter plot with cells colored by the estimated divergence (and other information if provided).
pl.acceleration(adata[, basis, color, frontier])	Scatter plot with cells colored by the estimated acceleration (and other information if provided).
pl.curl(adata[, basis, color, cmap, ...])	Scatter plot with cells colored by the estimated curl (and other information if provided).
pl.curvature(adata[, basis, color, frontier])	Scatter plot with cells colored by the estimated curvature (and other information if provided).
pl.jacobian(adata[, regulators, effectors, ...])	Scatter plot of Jacobian values across cells.
pl.jacobian_heatmap(adata, cell_idx[, ...])	Plot the Jacobian matrix for each cell or the average Jacobian matrix of the cells from input indices as a heatmap.
pl.sensitivity(adata[, regulators, ...])	Scatter plot of Sensitivity value across cells.
pl.sensitivity_heatmap(adata, cell_idx[, ...])	Plot the Jacobian matrix for each cell as a heatmap.

Regulatory network

pl.arcPlot(adata, cluster, cluster_name[, ...])	Arc plot of gene regulatory network for a particular cell cluster.
pl.circosPlot(network[, node_label_key, ...])	wrapper for drawing circos plot via nxviz >= 0.7.3
pl.circosPlotDeprecated(adata, cluster, ...)	Deprecated.
pl.hivePlot(adata, edges_list, cluster[, ...])	Hive plot of cell cluster specific gene regulatory networks.

Potential landscape

pl.show_landscape(adata, Xgrid, Ygrid, Zgrid)

Plot the quasi-potential landscape.

Cell fate

pl.fate(adata[, x, y, basis, color, ax, ...])	Draw the predicted integration paths on the low-dimensional embedding.
pl.fate_bias(adata, group[, basis, ...])	Plot the lineage (fate) bias of cells states whose vector field trajectories are predicted.

Heatmaps

pl.causality(adata, pairs_mat[, ...])	Plot the heatmap for the expected value z(t) given x and y data.
pl.comb_logic(adata, pairs_mat[, xkey, ...])	Plot the combinatorial influence of two genes x, y to the target z.
pl.plot_hill_function(adata[, pairs_mat, ...])	Plot the hill function curve generated by dynamo.pl.response.
pl.response(adata, pairs_mat[, xkey, ykey, ...])	Plot the lagged DREVI plot pairs of genes across pseudotime.

Predictions

pl.lap_min_time(adata[, basis, show_paths, ...])

Plot minimum time of the least action paths.

Save figures

pl.save_fig([path, prefix, dpi, ext, ...])

Save a figure from pyplot.

Moive (mv)

Note

animation class is internally to mv.animate_fates. See our animation classes here: animation

mv.animate_fates(adata[, basis, dims, ...])

Animating cell fate commitment prediction via reconstructed vector field function.

Simulation (sim)

Simple ODE vector field simulation

sim.toggle(ab[, t, beta, gamma, n])	Calculates the right-hand side (RHS) of the differential equations for the toggle switch system.
sim.Ying_model(x[, t])	network used in the potential landscape paper from Ying, et.

Gillespie simulation

sim.Gillespie([a, b, la, aa, ai, si, be, ...])	A simulator of RNA dynamics that includes RNA bursting, transcription, metabolic labeling, splicing, transcription, RNA/protein degradation
sim.Simulator([motif, seed_num, clip, cell_num])	Simulate the gene expression dynamics via deterministic ODE model
sim.state_space_sampler(ode, dim[, ...])	Sample N points from the dim dimension gene expression space while restricting the values to be between min_val and max_val.
sim.evaluate(reference, prediction[, metric])	Function to evaluate the vector field related reference quantities vs.

External (ext)

ext.ddhodge(adata[, X_data, layer, basis, ...])	Modeling Latent Flow Structure using Hodge Decomposition based on the creation of sparse diffusion graph from the reconstructed vector field function.
ext.enrichr(genes, organism[, background, ...])	Perform gene list enrichment with gseapy.
ext.scribe(adata[, genes, TFs, Targets, ...])	Apply Scribe to calculate causal network from spliced/unspliced, metabolic labeling based and other "real" time series datasets.
ext.coexp_measure(adata, genes, layer_x, layer_y)	Calculate co-expression measures, including mutual information (MI), pearson correlation, etc.
ext.scifate_glmnet(adata[, ...])	Reconstruction of regulatory network (Cao, et. al, Nature Biotechnology, 2020) from TFs to other target

Utilities

Package versions

get_all_dependencies_version([display])

Adapted from answer 2 in https://stackoverflow.com/questions/40428931/package-for-listing-version-of-packages-used-in-a-jupyter-notebook

Clean up adata

cleanup(adata[, del_prediction, del_2nd_moments])

clean up adata before saving it to a file

Figures configuration

configuration.set_figure_params([dynamo, ...])	Set resolution/size, styling and format of figures.
configuration.set_pub_style([scaler])	formatting helper function that can be used to save publishable figures