dgCMatrix inputs in the slots of input SCE objects.
- Significant speed optimisation on
scSEGIndex and add
scSEGIndex references after publication.
scMerge now has the
svd_k input that controls the number eigenvectors needed in the RUV step to allow fast approximation for large dataset.
- Now using
BiocSingular to manage all SVD components.
- Now automatically remove zeroes in the rows and columns of the SCE.
- Adding version restrictions on
SingleCellExperiment dependent packages.
plot_igraph would allow suppression of igraph output during unsupervised scMerge
- Column name must be non-NULL and without duplicates
- Resolved problems with only a single linking cell-type across multiple batches
scMerge 0.99 (development version)
- Updated ciation information due to PNAS acceptance.
- Fixed assignment based on feedbacks
- Increase code coverage to 85%.
- Updated vignette on SEGs and manuals
- Fixed spelling
- Added verbose option
- Code coverage at 75 percent (more tests on error handling needed)
- Fixed README
install_github vignette issue.
- Fixed pkgdown organisation issue.
- Major updates on the scReplicate function: more informative messages.
- Using cross-product of matrix to perform SVD to speed up calculations.
- Added testing scripts.
- Fixed vignette text output issues.
- Reduced data size in scMerge to pass BioC checks