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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.
- 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.
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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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