NEWS
rliger 2.0.1 (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 (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 in runPairwiseDEG()
- 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 (previously optimizeALS(unshared = TRUE)
) and online iNMF (previously online_iNMF()
) implementation to new package RcppPlanc with vastly improved performance. Now wrapped in runINMF()
, runUINMF()
and runOnlineINMF()
respectively, and all can be invoked with runIntegration()
.
- 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 (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