Man pages for gsdensity
Density-Based Gene Set Specificity Evaluation
| ce | cell embeddings for pbmc3k data |
| compute.cell.label | 4.2. binarize the label propagation probability in the cell... |
| compute.cell.label.df | similar to compute.cell.label; used when working with... |
| compute.db | this function is called by 'compute.kld' to aggregate the... |
| compute.grid.coords | 2. compute density of gene sets of interest 2.1 compute grid... |
| compute.jsd | 5. compute the specificity of gene set when cell partition... |
| compute.kld | 2.2 compute KL-divergence (some are adapted from... |
| compute.mca | 1. compute MCA embeddings |
| compute.nn.edges | 3. compute nearest neighbor graph for genes and cells This... |
| compute.spatial.kld | 6. find gene sets with spatial relevance |
| compute.spatial.kld.df | This function is to calculate how likely the cells relevant... |
| compute.spec | This is to calculate the similarity between: 1. the label... |
| compute.spec.single | This is to calculate the similarity between: 1. the label... |
| coords.df | mouse brain coords |
| el_nn_search | this function is called by 'compute.nn.edges' to convert... |
| gene.set.list | A gene set list containing multiple human GO gene sets |
| kde2d.weighted | based on... |
| pbmc.meta | pbmc3k meta |
| pbmc.mtx | pbmc3k matrix |
| run.rwr | 4.1 To calculate the label propagation probability for a gene... |
| run.rwr.list | result in a matrix (number of rows = number of cells; number... |
| sample.kld | this function is called by 'compute.kld' to calculate the... |
| sample.spatial.kld | this function is called by 'compute.spatial.kld' to calculate... |
| seed.mat | 4. compute label propagation from gene set to cells this... |
| seed.mat.list | this function is used when more than one 'seed sets' will be... |
| vectorized_pdist | from an excellent post:... |
| weight_df | mouse brain gene set activities |
