# Functional annotation-driven unsupervised clustering for single-cell data

## Documentation for package ‘ASURAT’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

add_metadata | Add metadata of variables and samples.
ASURAT | Functional annotation-driven unsupervised clustering of SingleCell data.
bubble_sort | Perform bubble sorting, counting the number of steps.
cluster_genesets | Cluster each functional gene set into three groups.
compute_sepI_all | Compute separation indices for each cluster against the others.
compute_sepI_clusters | Compute separation indices of sign scores for given two clusters.
create_signs | Define signs for strongly and variably correlated gene sets.
human_COMSig_eg | A list of small Cell Ontology and MSigDB databases for human.
human_GO_eg | A list of small Gene Ontology database for human.
human_KEGG_eg | A list of small KEGG database for human.
makeSignMatrix | Create a new SingleCellExperiment object for sign-by-sample matrices.
pbmcs_eg | A list of SingleCellExperiment objects made from sign-sample matrices.
pbmc_eg | A SingleCellExperiment object made from a gene expression table.
plot_dataframe3D | Visualize a three-dimensional data with labels and colors.
plot_multiheatmaps | Visualize multivariate data by heatmaps.
remove_samples | Remove samples based on expression profiles across variables.
remove_signs | Remove signs including too few or too many genes.
remove_signs_manually | Remove signs by specifying keywords.
remove_signs_redundant | Remove redundant signs using semantic similarity matrices.
remove_variables | Remove variables based on expression profiles across samples.
remove_variables_second | Remove variables based on the mean expression levels across samples.
select_signs_manually | Select signs by specifying keywords.
swap_pass | Perform one-shot adjacent swapping for each element.