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NEWS.md

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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 2.2.1.9002

  • Improved scalability of downstream analysis and visualization
    • Reduced the need of pre-calculated normalized data for performing Wilcoxon's test and producing feature expression plots
    • Normalized data will only be calculated on the fly from raw data and pre-stored size factor (obj$nUMI).
  • Added theme_axis_shortArrow() for tidy dimensional reduction plot axis theme.
  • Migrating to patchwork for multi-plot layouting. Mainly for the ease of alignment, legend collection, and subplot extraction.

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