Releases: carmonalab/scGate
Releases · carmonalab/scGate
scGate version 1.6.2
New in this version:
- Enable parallelization over a list of scGate models (in multi-classifier mode)
- Fix bug on parallelization when specifying BPPARAM
- Added cell ontology links for controlled cell type dictionary
- Update accessor functions to improve compatibility with Seurat v5
scGate version 1.6
New in this version:
- Addresses compatibility with Assay5 Seurat assays.
- Enables parallelization over a list of models, in multi-classifier mode (see
BPPARAM
) - Uses new implementation of
UCell::SmoothKNN()
to smooth signature scores between neighboring cells. Neighbor cells are weighted by$(1-smooth.decay)^n$ , where n is the n-th neighbor in PCA space, andsmooth.decay
is a parameter between 0 and 1.
scGate version 1.4
New in this version:
- scGate is now on CRAN! it can be installed using
install.packages("scGate")
- The function
get_scGateDB()
now writes totempdir()
by default. To recover the behavior of previous versions, setdestination="./scGateDB"
or to some other local directory - Log out fraction of "Pure" cells instead of "Impure" cells
- Fixed bug on kNN smoothing with too few remaining cells
- Improved documentation and examples
scGate version 1.2
New features in version 1.2.0
- Simultaneously evaluate multiple gating models, given as a list to
model
parameter- Returns individual gatings as well as a combined cell type annotation from all the models (scGate_multi metadata column)
- Allows running scGate as a multi-class classifier and annotate cell types in a dataset
- New
reduction
parameter- Allows nearest-neighbor smoothing on an existing dimensionality reduction (e.g. "pca" or "harmony")
- Can significantly speed up computation time and annotation of integrated objects
- Uses Bioconductor version of UCell
Zenodo preservation and DOI citation in journal publication
v1.0.1 in README include links to atac & adt demos