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rliger Next
- Ability to reorganize datasets
- Allow doing something like
reorganize(ligerObj, variable = "somethingNotDataset") andresulting in a new liger object with different ligerDatasetgrouping.
- Ability to do downstream analysis on H5 data
- Pseudo-bulk should be easy because we are just aggregatingcells.
- Wilcoxon might be a bit harder because ranks are calculated per genebut the H5 sparse data is column majored. Might need to find a faston-disk transposition method.
rliger 2.2.1
- Added naive GSEA analysis on factor gene loading (W) to test if anyknown gene sets (e.g. cell cycle) is enriched in any factor. Implementedin
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 millioncells using slightly more time than in-memory version, requiring onlylaptop-level memory.
- Added 10X H5 data and H5AD loading function that loads the data intoregular dgCMatrix in memory or the DelayedArray representation backed ondisk, the latter is used for on-disk iNMF implementation.
- Added
selectBatchHVG() which implements another HVGselection strategy, credit to SCIB - Adding
suggestK() back with new methodology - Clarified optimal
runGOEnrich() workflow and added foldenrichment 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 loadingalignment method - Added
plotProportionBox() for visualizing compositionalanalysis - Added
plotClusterGeneViolin() for visualizing geneexpression in clusters - Added
plotBarcodeRank() for basic QC visualization - Added
plotPairwiseDEGHeatmap() for visualizing pairwiseDEG results - Added
plotGODot() for visualizing GO enrichmentresults - Added
calcNMI() for evaluating clustering resultsagainst ground truth - Added
ligerToH5AD() allowing reticulate/Python freeexport of liger object to H5AD format. This is presented in extensionsource code (i.e. not loaded withlibrary(rliger)). - Added organism support in
runGeneralQC() and refinedhemoglobin gene matching regex pattern. - Optimized DE test memory usage scalability for both pseudo-bulkmethod and wilcoxon test
- Optimized
plotProportionPie() by adding argumentcircleColors - Optimized
plotVolcano() text annotation positioning andgene highlighting logic. - Optimized visualization function additional argumentdocumentation
- Changed
runMarkerDEG() andrunPairwiseDEG() default method from"wilcoxon" to"pseudoBulk" - Fixed
runMarkerDEG(method = "pseudobulk") bug inassigning 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-existingdependencies
- Fixed file access issue when checking on CRAN
- Updated installed data file
system.file("extdata/ctrl.h5", "extdata/stim.h5") to be ofstandard 10X H5 format - Updated
quantileNorm() automatic reference selectionaccording to #297 - Other minor fixes (including #308)
rliger 2.0.0
- Added
ligerDataset class for per-dataset informationstorage, with inheritance for specific modalities - Added a number of plotting functions with clear function names anduseful functionality
- Added Leiden clustering method, now as default rather thanLouvain
- Added pseudo-bulk DEG method
- Added DEG analysis with one-vs-rest marker detection in
runMarkerDEG() and pairwise comparison inrunPairwiseDEG() - Added gene name pattern for expression percentage QC metric
- Added native Seurat object support for the core integrationworkflow
- 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(previouslyoptimizeALS(unshared = TRUE)) and online iNMF(previouslyonline_iNMF()) implementation to new packageRcppPlanc with vastly improved performance. Now wrapped inrunINMF(),runUINMF() andrunOnlineINMF() respectively, and all can be invoked withrunIntegration(). - Updated H5AD support to match up with Python anndata package 0.8.0specs
- Renamed many function/argument names to follow camelCase style,original names are still available while deprecation warnings areissued
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
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