Changelog • bixverse

bixverse 0.3.1

Minor dependency update on the Rust side. Bumped versions to improved Rust crates.

The big one… First, shift of versioning + release of full single cell analysis suite. See below for more details.

Full refactor of the Rust code, so it lives in its own crate
Single cell officially released:
- Class with getters that leverages on-disk storage of counts and a streaming engine to enable memory-friendly analysis of millions of cells.
- I/O helpers that can read mtx outputs, h5ad, h5ad with only normalised counts, multiple h5ad and conversion from Seurat implemented.
- Fully functional suite of pre-processing functions: proportion of gene sets, proportion of Top N genes of overall counts, HVG detection, PCA (with sparse solving avoiding densification), multiple kNN backends for different use-cases, sNN generation and Leiden community detection.
- Three different batch correction methods implemented: BBKNN, fastMNN and Harmony.
- Various analysis methods for single cell implemented: AUCell, GeneModuleScoring, VISION, Hotspot, SCENIC and miloR implementations.
- Metacell generation: hdWGCNA bootstrap approach, SuperCells and SEACells.
- Large number of convenience functions.
Sister package started with plotting functions.
Package with very fast 2D embedding methods also ready as a sister package – check out manifoldsR.

Mitch multi contrast enrichment implemented in Rust.
Rework and refactor of sub modules in the Rust code.
Additional Rust functions for set similarity across a list of items in R.
QC function for the bulk DGE class split into qc_bulk_dge() and normalise_bulk_dge().
Bulk DGE function split into calculate_dge_limma() and calculate_dge_hedges().
Splitting by correlation sign and Eigengene calculation added for CoReMo.
SNF algorithm added from Wang et al..
Spectral clustering methods implemented in Rust.
Breaking change: rs_set_similarity_list() renamed to rs_set_similarity_list2(). The former now takes a single list and calculates set similarity across all permutations of elements.
Breaking change: preprocess_bulk_dge() and calculate_all_dges() have been removed.

Constrained PageRank implementation added.
Improved synthetic data for correlation-based gene module detection.
Improved tests for ICA, CoReMo and graph-based correlation modules.
Various distance calculations accelerated in Rust.
Rust-based personalised PageRank implementations now support weighted graphs.
Bug fixes for the graph-based correlation methods.
Fixed export bugs for some plotting functions.
Breaking change: interface to Rust-based personalised PageRank calculations may break due to the addition of a weights parameter.

Rework of the ontology class with Wang similarity added as an additional measure.
Rework of the genetic community detection class and diffusion methods, including permutation-based testing for diffusions.
Rework of the ICA code with a testing suite added for the ICA class.
Reciprocal best hit method based on correlations added; an additional parameter is now required specifying whether to use set similarity or correlation-based similarity.
Vignettes added for various methods.
GSVA and ssGSEA implemented in Rust.
Rust code reworked in various places for improved performance.
Mutual information calculations implemented in Rust.
Improvements to the synthetic data.
Bug fixes for the graph-based correlation methods.
Breaking change: ontology class functions and methods have been modified heavily and may be breaking.
Breaking change: community detection method has been updated; old code may not work.
Breaking change: ICA detection functions and methods have been updated and may break existing code.

TOM implemented in Rust for correlation-based module detection.
CoReMo-based gene module detection added.
Breaking change: cor_module_check_res() renamed to cor_module_graph_check_res() and cor_module_final_modules() renamed to cor_module_graph_final_modules().

fgsea multi level method implemented; n_more_extreme is now returned by GSEA functions.
RBF function implementations added for R matrices.

Semantic similarities for ontologies added.
Speed improvements in various Rust functions via reduced memory copying and use of lifetimes.
Package stability improved with tests powered by tinytest.
Set similarity Rust functions exposed.
DGE class added for Limma Voom differential gene expression calculations.
Wrapper functions added to load h5ad objects into R memory.
Traditional GSEA and fgsea simple ported into Rust.
Bug fix: future::plan() for iterating over resolutions in reciprocal best hit graph generation.
Bug fix: hypergeometric calculations and RBH graph.
Breaking change: community_detection() now uses params_community_detection() for parameters.

Hypergeometric tests for gene set analysis for single or lists of target gene sets.
Gene ontology aware hypergeometric test for GO analysis.
Network diffusion methods based on personalised PageRank (single and tied diffusion).
Community detection algorithms on top of diffusion scores.
Reciprocal best hit graphs using set similarities between gene modules from different data sets or methods.
Contrastive PCA implementation for gene module detection.
Differential correlation-based methods for gene module detection using network-based graph community detection.
Independent component analysis with stabilised versions.
Helper functions for Hedge’s G effect size and OpenTargets score summarisation.