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NEWS.md

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rliger Next

  • 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.

rliger 2.1.0.9003

  • 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

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