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NEWS

• 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.

• Implemented highly efficient on-disk iNMF that scales to a million cells using slightly more time than in-memory version, requiring only laptop-level memory.
• Added 10X H5 data and H5AD loading function that loads the data into regular dgCMatrix in memory or the DelayedArray representation backed on disk, the latter is used for on-disk iNMF implementation.
• Added selectBatchHVG() which implements another HVG selection strategy, credit to SCIB
• Adding suggestK() back with new methodology
• Clarified optimal runGOEnrich() workflow and added fold enrichment metric in the returned result
• Fixed important bug in online iNMF scenario 2
• 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

• 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

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