rliger Release v2.0.0

rliger 2.0.0

• 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.
• 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