Man pages for keita-iida/ASURATBI
A pipeline especially built for computing several single-cell datasets
| add_metadata | Add metadata of variables and samples. |
| ASURATBI | A pipeline especially built for computing several single-cell... |
| 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... |
| compute_sepI_clusters | Compute separation indices of sign scores for given two... |
| 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... |
| pbmc_eg | A SingleCellExperiment object made from a gene expression... |
| pbmcs_eg | A list of SingleCellExperiment objects made from sign-sample... |
| plot_dataframe3D | Visualize a three-dimensional data with labels and colors. |
| plot_elasticTree3D | Plot elastic trees computed by MERLoT. |
| plot_multiheatmaps | Visualize multivariate data by heatmaps. |
| plot_pseudotime3D | Plot pseudotime computed by MERLoT. |
| plot_pseudotimecourse_woTree | Plot pseudotime courses of sign scores without elastic tree. |
| plot_pseudotimecourse_wTree | Plot pseudotime courses of sign scores with elastic tree. |
| 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... |
| select_signs_manually | Select signs by specifying keywords. |
| swap_pass | Perform one-shot adjacent swapping for each element. |
