Releases: welch-lab/liger
Releases · welch-lab/liger
rliger Release v2.0.1
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 Release v2.0.0
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 inrunPairwiseDEG()
- 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. - Changed
liger
object class structure - Moved iNMF (previously
optimizeALS()
), UINMF (previouslyoptimizeALS(unshared = TRUE)
) and online iNMF (previouslyonline_iNMF()
) implementation to new package RcppPlanc 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 0.8.0 specs
- Renamed many function/argument names to follow camelCase style, original names are still available while deprecation warnings are issued
rliger Release v1.0.1
- 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
LIGER with UINMF
Added functionality related to UINMF, allowing "mosaic integration" incorporating both shared and unshared features
Version 1.0.0
Changes:
- LIGER package is now installed as
rliger
(Please uselibrary(rliger)
to load it in R).
Additions:
- Iterative single-cell multi-omic integration using online iNMF (
online_iNMF
) on data saved in HDF5 format.
Version 0.5.0
Changes:
- Bug fixes for R CMD check
- Optimize dependencies
Version 0.5.0.9000
Changes:
- Update
imputeKNN
with faster algorithm - Add new function
runWilcoxon
for Wilcoxon test; - Add new functions for calculating the correlation between genes and peaks,
linkGenesAndPeaks
,makeInteractTrack
- Add
quantile_norm
, a faster cpp inplementation ofquantileAlignSNF
- Add
louvainCluster
for performing Louvain clustering; - Minor updates to
optimizeALS
,plotGeneLoading
- Minor fix for dependency
Version 0.4.1
Fixes bugs in plotFeature in v0.4.0
Version 0.4.0
Changes:
- Update liger object to include cell metadata in cell.data slot (default nUMI, nGene, etc)
- Add new visualization functions plotFeature, plotGeneLoadings
- Add faster Rcpp based implementations of selectGenes and scaleNotCenter
- Add basic unit tests
- Minor updates to plotGene
- Minor fixes for runTSNE, selectGenes
- Minor updates to liger object structure
Version 0.3.0
Changes:
- Improve suggestLambda and suggestK functionality and add support for progress bar
- Add dependency to doSNOW, remove doParallel
- Add Read10X function
- Add plotClusterFactors function
- Add convertOldLiger function
- Minor performance improvement in utility function MergeSparseDataAll
- Minor updates to seuratToLiger and ligerToSeurat
- Minor documentation updates