Release Notes

Version 0.2.3 Feb 13, 2021

  • tl.recover_dynamics: Multicore implementation thanks to M Klein, Y Schaelte, P Weiler
  • CI now runs on GitHub Actions

New utility functions:

  • utils.gene_info: Retrieve gene information from biothings client.
  • utils.convert_to_ensembl and utils.convert_to_gene_names: Converting ensembl IDs into gene names and vice versa.

Version 0.2.2 July 22, 2020

  • tl.paga: PAGA graph with velocity-directed edges.
  • Black code style

Version 0.2.1 May 28, 2020

Bugfixes:

  • Correct identification of root cells in tl.latent_time thanks to M Lange
  • Correct usage of latent_time prior in tl.paga thanks to G Lubatti

Version 0.2.0 May 12, 2020

New vignettes:

  • RNA velocity basics
  • Dynamical Modeling
  • Differential Kinetics

Tools:

  • tl.differential_kinetic_test: introduced a statistical test to detect different kinetic regimes.
  • tl.rank_dynamical_genes: introduced a gene ranking by cluster-wise likelihoods.
  • tl.paga: introduced directed PAGA graph

Plotting:

  • pl.scatter enhancements: linear and polynomical fits, gradient coloring
  • pl.proportions: Pie and bar chart of spliced/unspliced proprtions.
  • GridSpec: multiplot environment.

Version 0.1.20 Sep 5, 2019

Tools:

  • tl.recover_dynamics: introduced a dynamical model inferring the full splicing kinetics, thereby identifying all kinetic rates of transcription, splicing and degradation.
  • tl.recover_latent_time: infers a shared latent time across all genes based on the learned splicing dynamics.

Plotting:

  • pl.scatter enhancements: multiplots, rugplot, linear and polynomial fits, density plots, etc.
  • pl.heatmap: heatmap / clustermap of genes along time coordinate sorted by expression along dynamics.

Preprocessing:

  • New attributes in pp.filter_genes: min_shared_counts and min_shared_genes.
  • Added fast neighbor search method: Hierarchical Navigable Small World graphs (HNSW)

Version 0.1.14 Dec 7, 2018

Plotting:

  • New attriutes arrow_length and arrow_size for flexible adjustment of embedded velocities.
  • pl.velocity_graph: Scatter plot of embedding with cell-to-cell transition connectivities.
  • pl.velocity_embedding_stream: Streamplot visualization of velocities.
  • Improve visualization of embedded single cell velocities (autosize, colors etc.)

Tools:

  • tl.cell_fate: compute cell-specific terminal state likelihood
  • New attribute approx=True in tl.velocity_graph to enable approximate graph computation by performing cosine correlations on PCA space.

Preprocessing:

  • Automatically detect whether data is already preprocessed.

Version 0.1.11 Oct 27, 2018

Plotting:

  • settings.set_figure_params(): adjust matplotlib defaults for beautified plots
  • improved default point and arrow sizes; improved quiver autoscale
  • enable direct plotting of

Tools:

  • tl.velocity_confidence: Added two confidence measures ‘velocity_confidence’ and ‘velocity_confidence_transition’.
  • tl.rank_velocity_genes: Added functionality to rank genes for velocity characterizing groups using a t-test.
  • New attribute perc in tl.velocity enables extreme quantile fit, e.g. set perc=95.
  • New attribute groups in tl.velocity enables velocity estimation only on a subset of the data.
  • Improved tl.transition_matrix by incorporating self-loops via self_transitions=True and state changes that have negative correlation with velocity (opposite direction) via use_negative_cosines=True

Utils:

  • utils.merge to merge to AnnData objects such as already existing AnnData and newly generated Loom File.

Version 0.1.8 Sep 12, 2018

Plotting:

  • support saving plots as pdf, png etc.
  • support multiple colors and layers
  • quiver autoscaling for velocity plots
  • attributes added: figsize and dpi

Preprocessing:

  • filter_and_normalize() instead of recipe_velocity()
  • normalization of layers is done automatically when computing moments

Tools:

  • terminal_states: computes root and end points via eigenvalue decomposition thanks to M Lange

Version 0.1.5 Sep 4, 2018

  • Support writing loom files
  • Support both dense and sparse layers
  • Plotting bugfixes
  • Added pp.recipe_velocity()

Version 0.1.2 Aug 21, 2018

First alpha release of scvelo.