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.. automodule:: scvelo

API

Import scVelo as:

import scvelo as scv

After reading the data (scv.read) or loading an in-built dataset (scv.datasets.*), the typical workflow consists of subsequent calls of preprocessing (scv.pp.*), analysis tools (scv.tl.*) and plotting (scv.pl.*). Further, several utilities (scv.utils.*) are provided to facilitate data analysis.

Read / Load

.. autosummary::
   :toctree: .

   read
   read_loom


Preprocessing (pp)

Basic preprocessing (gene selection and normalization)

.. autosummary::
   :toctree: .

   pp.filter_genes
   pp.filter_genes_dispersion
   pp.normalize_per_cell
   pp.log1p
   pp.filter_and_normalize

Moments (across nearest neighbors in PCA space)

.. autosummary::
   :toctree: .

   pp.pca
   pp.neighbors
   pp.moments


Tools (tl)

Clustering and embedding (more at scanpy-docs)

.. autosummary::
   :toctree: .

   tl.louvain
   tl.umap

Velocity estimation

.. autosummary::
   :toctree: .

   tl.velocity
   tl.velocity_graph
   tl.velocity_embedding

Dynamical modeling

.. autosummary::
   :toctree: .

   tl.recover_dynamics
   tl.differential_kinetic_test

Dynamical genes

.. autosummary::
   :toctree: .

   tl.rank_velocity_genes
   tl.rank_dynamical_genes


Pseudotime and trajectory inference

.. autosummary::
   :toctree: .

   tl.terminal_states
   tl.velocity_pseudotime
   tl.latent_time
   tl.paga

Further tools

.. autosummary::
   :toctree: .

   tl.velocity_clusters
   tl.velocity_confidence
   tl.score_genes_cell_cycle


Plotting (pl)

Base scatter plot

.. autosummary::
   :toctree: .

   pl.scatter

Velocity embeddings

.. autosummary::
   :toctree: .

   pl.velocity_embedding
   pl.velocity_embedding_grid
   pl.velocity_embedding_stream

Velocity graph

.. autosummary::
   :toctree: .

   pl.velocity
   pl.velocity_graph
   pl.paga

Further plotting

.. autosummary::
   :toctree: .

   pl.proportions
   pl.heatmap
   pl.hist


Datasets

.. autosummary::
   :toctree: .

   datasets.pancreas
   datasets.dentategyrus
   datasets.forebrain
   datasets.dentategyrus_lamanno
   datasets.gastrulation
   datasets.gastrulation_e75
   datasets.gastrulation_erythroid
   datasets.bonemarrow
   datasets.pbmc68k
   datasets.simulation


Utils

Get data by key

.. autosummary::
   :toctree: .

   get_df

Get gene info

.. autosummary::
   :toctree: .

   utils.gene_info

Data preparation

.. autosummary::
   :toctree: .

   utils.cleanup
   utils.clean_obs_names
   utils.merge
   utils.show_proportions

Getters

.. autosummary::
   :toctree: .

   utils.get_moments
   utils.get_transition_matrix
   utils.get_cell_transitions
   utils.get_extrapolated_state

Converters

.. autosummary::
   :toctree: .

   utils.convert_to_ensembl
   utils.convert_to_gene_names

Least squares and correlation

.. autosummary::
   :toctree: .

   utils.leastsq
   utils.vcorrcoef
   utils.test_bimodality


Settings

.. autosummary::
   :toctree: .

   set_figure_params