0.3.2

version 0.3.2 (11-July-2024)

• change engine for conversion between rds and h5ad file formats to sceasy.

0.3.1

corrected problems in annotatePairing to give correct classification of number of H/L BCR sequences annotated to each cell barcode.

0.3.0

• unit tests written and tested
• getIsotype function to allow grouping of cells by sterile transcripts they express
• mergeIgHCountsToSeurat function to process the called productive/sterile transcript counts and merge into the Seurat object (wrap around code to fill in the matrix with 0 for missing cells)

0.2.1

• fixed issues re distributed computing in python across MacOS and Windows.
• added functions for basic scRNA-seq data preprocessing (normalise_dimreduce) which includes customisable pruning of variably expressed genes, collapse VDJ (or other genes) into metagenes etc (collapseIntoMetaGenes).

Full Changelog: 0.2.0...0.2.1

0.2.0

• removed velocyto.R dependency to avoid installation problems.
• fixed minor issues for cross-platform (MacOS / Linux) installation and use.
• fixed issues with multiprocessing in TPT calculations.
• added a NEWS.md file to track changes to the package.
• functional vignette site via pkgdown.

Full Changelog: 0.1.1...0.2.0

0.1.1

• added new functions for plotting TPT isotype results.
• NMF-based calculation of CSR potential.
• functions to merge repertoire.
• plot arrow-style velocity streams a-la-scVelo.

Full Changelog: https://github.com/Fraternalilab/sciCSR/commits/0.1.1