Version 0.2.5 Oct 14, 2022¶
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).
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¶
Landing page and two notebooks accompanying the perspectives manuscript at MSB.
New datasets: Gastrulation, bone marrow, and PBMCs.
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.
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¶
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¶
RNA velocity basics
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
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¶
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.
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.
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¶
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.)
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.
Automatically detect whether data is already preprocessed.
Version 0.1.11 Oct 27, 2018¶
settings.set_figure_params(): adjust matplotlib defaults for beautified plots
improved default point and arrow sizes; improved quiver autoscale
enable direct plotting of
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.merge to merge to AnnData objects such as already existing AnnData and newly generated Loom File.
Version 0.1.8 Sep 12, 2018¶
support saving plots as pdf, png etc.
support multiple colors and layers
quiver autoscaling for velocity plots
attributes added: figsize and dpi
filter_and_normalize() instead of recipe_velocity()
normalization of layers is done automatically when computing moments
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
Version 0.1.2 Aug 21, 2018¶
First alpha release of scvelo.