Changelog
Source:NEWS.md
rliger 2.0.1
CRAN release: 2024-04-04
- Fixed wrong UINMF aborting criteria
- Fixed example/test skipping criteria for non-existing dependencies
- Fixed file access issue when checking on CRAN
- Updated installed data file
system.file("extdata/ctrl.h5", "extdata/stim.h5")
to be of standard 10X H5 format - Updated
quantileNorm()
automatic reference selection according to #297 - Other minor fixes (including #308)
rliger 2.0.0
CRAN release: 2024-03-20
- Added
ligerDataset
class for per-dataset information storage, with inheritance for specific modalities - Added a number of plotting functions with clear function names and useful functionality
- Added Leiden clustering method, now as default rather than Louvain
- Added pseudo-bulk DEG method
- Added DEG analysis with one-vs-rest marker detection in
runMarkerDEG()
and pairwise comparison inrunPairwiseDEG()
- Added gene name pattern for expression percentage QC metric
- Added native Seurat object support for the core integration workflow
- Added a documentation website built with pkgdown
- Added new iNMF variant method, consensus iNMF (c-iNMF), in
runCINMF()
. Not stable. - Added GO enrichment dowsntream analysis in
runGOEnrich()
- Changed
liger
object class structure - Moved iNMF (previously
optimizeALS()
), UINMF (previouslyoptimizeALS(unshared = TRUE)
) and online iNMF (previouslyonline_iNMF()
) implementation to new package RcppPlanc with vastly improved performance. Now wrapped inrunINMF()
,runUINMF()
andrunOnlineINMF()
respectively, and all can be invoked withrunIntegration()
. - Updated H5AD support to match up with Python anndata package 0.8.0 specs
- Renamed many function/argument names to follow camelCase style, original names are still available while deprecation warnings are issued
rliger 1.0.1
CRAN release: 2023-11-08
- Allow setting mito pattern in
getMitoProportion()
#271 - Fix efficiency issue when taking the log of norm.data (e.g.
runWilcoxon
) - Add runable examples to all exported functions when possible
- Fix typo in online_iNMF matrix initialization
- Adapt to Seurat5
- Other minor fixes