rliger Next

• 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.

rliger 2.2.1

• Added naive GSEA analysis on factor gene loading (W) to test if any known gene sets (e.g. cell cycle) is enriched in any factor. Implemented in factorGSEA().
• Added dense data loading support for H5AD files
• Optimized obs metadata parsing for H5AD files
• Fixed ggplot2 color picking when coloring by logical value
• Fixed H5AD file layer detecting bug
• Fixed some other minor bugs

rliger 2.2.0

• 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

rliger 2.1.0

• 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

rliger 2.0.1

• 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

• 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

• 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