Release Notes

Version 0.2.5 Oct 14, 2022

Changes:

  • Catch non-positive parameter values and raise a ValueError if necessary (PR 614).
  • get_mean_var uses the same size parameter for mean and variance (PR 698).

Bugfixes:

  • filter_genes now works with adata.layers[‘unspliced’] being sparse and adata.layers[‘spliced’] dense (PR 537).
  • show_proportions actually considers the layer “ambiguous” if present (PR 587).
  • Fix calculation of Pearson’s correlation in csr_vcorrcoef (PR 679).
  • Fix get_mean_var to work with sparse input and ignore_zeros=True (PR 698).
  • Fix bug in neighbor calculation (PR 797).
  • Fix optimization.py::get_weight to work with numeric, non-integer values (PR 839).
  • Fix inference with fit_scaling=False (PR 848).
  • Fix saving of velocity embedding stream (PR 900).
  • Fix Pandas’ display precison when passed to get_df (PR 907).

Version 0.2.4 Aug 26, 2021

Perspectives:

  • Landing page and two notebooks accompanying the perspectives manuscript at MSB.
  • New datasets: Gastrulation, bone marrow, and PBMCs.

New capabilities:

  • Added vignettes accompanying the NBT manuscript.
  • Kinetic simulations with time-dependent rates.
  • New arguments for tl.velocity_embedding_stream (PR 492).
  • Introduced automated code formatting flake8 and isort (PR 360, PR 374).
  • tl.velocity_graph parallelized (PR 392).
  • legend_align_text parameter in pl.scatter for smart placing of labels without overlapping.
  • Save option for pl.proportions.

Bugfixes:

  • Pinned sphinx<4.0 and nbsphinx<0.8.7.
  • Fix IPython import at CLI.

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.