Man pages for reggenlab/UniPath
UniPath provides robust statistical methods to represent every single cell using pathway and gene-set enrichment scores. It can be used with both single cell RNA-seq and single cell ATAC-seq profile with scalability for atlas scale data-sets. Unipath comes with several features like psuedo-temporal ordering using pathway scores and unconventional way of enumerating differences between two cell populations.
| adjust | Adjusting of combine p-values using null model |
| binorm | Conversion of non-zero gene FPKM value into p-value using... |
| class1 | Finding how many times nearest neighbor of cells in each... |
| combine | Combining P values |
| difcoccur | Differential coenriched pathways |
| distance | Two level shrinkage of distance matrix based on nearest... |
| dist_clust | Hierarchal clustering of pathway score matrix |
| drimpute | Imputation of scATAC-seq profiles |
| global_access | Global accessibility score calculation |
| gradient | Showing gradient or continuum of pathways on minimum spanning... |
| index | Finding K nearest neighbour |
| KNN | Getting cluster numbers for each of the nearest neighbor of a... |
| minimum_spanning_tree | Finding minimum spanning tree using shrinked distance matrix |
| mst.plot.mod | Plotting minimum spanning tree |
| nearest_gene | Generation of foreground file |
| runGO | Calculating pathway enrichment scores for scATAC-seq profiles |
| temporaldif | Differential Pathways |
