CHANGELOG.md

In kharchenkolab/cacoa: Case-Control Analysis Tools for Single-Cell RNA-Seq

[Upcoming]

Added

• Parameter assay.name for Seurat objects in Cacoa$new to allow selecting different assays
• cao$plotMetadataSeparation function
• sample.subset parameter for plotSampleDistances and estimateMetadataSeparation
• method="UMAP" for cao$plotSampleDistances, which should work much better on larger sample collections (>50 or so)
• Updated documentation for most functions in R6 class object
• Updated functionality (estimations and plotting) for ontologies, especially GSEA and DO as well as families
• Added parameter only.family.children to plotOntologySimilarities
• Added parameter families to plotNumOntologyTermsPerType
• Added example data for testing
• Several minor bug fixes

Changed

• Improved algorithm for metadata separation estimation. The effect should be noticeable only on large sample sizes.

[0.4.0] - 2022-05-May

Changed

• Small bug fixes and usability improvements
• Renamed options for dist.type in estimateExpressionShiftMagnitudes to match the paper figure
• Renamed inner estimateExpressionShiftMagnitudes to estimateExpressionChange (CRAN requirement)
• Renamed p.adj.cutoff to p.adj in estimateDEStabilityPerGene for consistency with other functions

kharchenkolab/cacoa documentation built on Nov. 8, 2024, 6:06 a.m.