NEWS.md
In MacoskoLab/liger: Linked Inference of Genomic Experimental Relationships

Standardized H5 IO specification that can be shared with other platforms.
Will move to use HDF5Array (TENxMatrix, H5ADMatrix)/ or BPCells for backed data representation, depending on easiness, cleanliness and future-sustainability of the implementation and cross-platform interoperability.
Read feature metadata (e.g. id, name, ...) if available; Allow setting "id" as rownames, "name" for visualization.
rawData - coming from the original input, read only (qc filtering should be just stored in the object, no IO)
preprocessing metrics - nUMI, nGene and etc, still go "chunkApply" so the file is read only once
normData - delayed computed data from rawData, no on disk representation
scaleData - new on-disk file and then create object back, because RcppPlanc won't be able to handle delayed computation
Ability to reorganize datasets
Allow doing something like reorganize(ligerObj, variable = "somethingNotDataset") and resulting in a new liger object with different ligerDataset grouping.
Ability to do downstream analysis on H5 data
Pseudo-bulk should be easy because we are just aggregating cells.
Wilcoxon might be a bit harder because ranks are calculated per gene but the H5 sparse data is column majored. Might need to find a fast on-disk transposition method, which would also enhance RcppPlanc performance when running ANLS on H5 data.

Added selectBatchHVG() which implements another HVG selection strategy, credit to SCIB
Fixed multiple problems related to ATAC analysis
Fixed Wilcoxon rank-sum test bug when using ATAC peak counts
Fixed gene coordinate parsing bug from BED file
Optimized peak parsing speed

Added centroidAlign() for new cell factor loading alignment method
Added plotProportionBox() for visualizing compositional analysis
Added plotClusterGeneViolin() for visualizing gene expression in clusters
Added plotBarcodeRank() for basic QC visualization
Added plotPairwiseDEGHeatmap() for visualizing pairwise DEG results
Added plotGODot() for visualizing GO enrichment results
Added calcNMI() for evaluating clustering results against ground truth
Added ligerToH5AD() allowing reticulate/Python free export of liger object to H5AD format. This is presented in extension source code (i.e. not loaded with library(rliger)).
Added organism support in runGeneralQC() and refined hemoglobin gene matching regex pattern.
Optimized DE test memory usage scalability for both pseudo-bulk method and wilcoxon test
Optimized plotProportionPie() by adding argument circleColors
Optimized plotVolcano() text annotation positioning and gene highlighting logic.
Optimized visualization function additional argument documentation
Changed runMarkerDEG() and runPairwiseDEG() default method from "wilcoxon" to "pseudoBulk"
Fixed runMarkerDEG(method = "pseudobulk") bug in assigning pseudo-replicates, and optimized error/warning signaling.
Fixed bug in calcAlignment(), subsetMemLigerDataset(), cellMeta()
Fixed bug in old version updating functions

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)

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