Man pages for ParkerICI/scgraphs
Analyzing single-cell data using graphs
| add_inter_clusters_connections | Add connections between cluster nodes |
| add_vertices_to_landmarks_graph | Add cluster vertices to a landmark graph |
| build_graph | Builds a graph from a data.frame of nodes |
| build_umap_graph | Builds a UMAP graph |
| complete_forceatlas2 | Performs a Complete cycle of ForceAtlas2 |
| cosine_similarity_from_matrix | Calculate cosine similarity between a vector and the rows of... |
| cosine_similarity_matrix | Calculate cosine similarity between the rows of a matrix |
| distance_from_attractor_hard_filter | Remove connections to landmark nodes based on an expression... |
| downsample_by | Downsample an input data.frame |
| filter_matrix | Filter a matrix based on a threshold value |
| filter_matrix_by_rank | Filter a matrix based on the rank of the values in each row |
| get_distances_from_landmarks | Calculate (and filter) disatances between cluster and... |
| get_highest_scoring_edges | Add information about edge types and highest scoring edges |
| get_scaffold_map | Creates a Scaffold map |
| get_unsupervised_graph | Builds an unsupervised force-directed graph |
| get_unsupervised_graph_from_files | Builds an unsupervised graph starting from a list of input... |
| layout_forceatlas2 | ForceAtlas2 force-directed layout |
| load_landmarks | Load landmark populations from a list of FCS files |
| load_landmarks_from_dir | Load landmark populations from a directory |
| run_scaffold_analysis | High level wrapper for performing a Scaffold analysis |
| vite | vite |
| vite_GUI | Start an analysis from the GUI |
| write_clusters_data | Write clustering output |
| write_graph | Write a graph as GraphML file |
| write_landmarks_data | Write landmarks data |
| write_scaffold_output | Write the result of a Scaffold analysis |
