Man pages for JEFworks/MERingue
Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with non-uniform cellular densities
| BCL | Spatial transcriptomics transcriptomics of 4 breast cancer... |
| cleanCounts | Filter a counts matrix |
| drosophila | Drosophila embryo aligned ISH from the in situ database... |
| filterSpatialPatterns | Filter for spatial patterns |
| getBnn | Nearest background neighbor |
| getClusters | Get transcriptional clusters by graph-based clustering |
| getCrossLayerNeighbors | Nearest neighbors across layers |
| getDifferentialGenes | Differential expression analysis (adapted from PAGODA2) |
| getInterCellTypeWeight | Filter adjacency weight matrix to between two subsets of... |
| getKnn | K nearest neighbors |
| getMnn | Mutual nearest neighbors |
| getOverdispersedGenes | Get overdispersed genes whose expression variance is higher... |
| getPv | Helper function to get p-value from value and distribution... |
| getSpatiallyInformedClusters | Get spatially informed clusters by weighting graph-based... |
| getSpatialNeighbors | Adjacency weight matrix by Delaunay triangulations in 2D or... |
| getSpatialPatterns | Identify spatial clusters |
| groupSigSpatialPatterns | Group significant spatial patterns |
| interCellTypeSpatialCrossCor | Tests for inter-cell-type spatial cross-correlation between... |
| interpolate | Gridded bivariate interpolation For interpolating primary... |
| lisaTest | Local indicators of spatial association |
| makeApp | Make a shiny app to interactively explore data |
| MERINGUE | MERINGUE |
| mOB | Spatial transcriptomics transcriptomics of the mouse... |
| moranPermutationTest | Derive Moran's I p-value using permutation testing |
| moranTest | Spatialy autocorrelation by Moran's I in C++ |
| moranTest_DEPRECATED | Spatialy autocorrelation by Moran's I DEPRECATED! Use... |
| mouseCoronal | Visium 10X Spatial Transcriptomics data of an adult mouse... |
| mPOA | MERFISH data of the mouse pre-optic region for a female naive... |
| normalizeCounts | Normalizes counts to CPM |
| plotEmbedding | Plot 2D embedding |
| plotInterCellTypeSpatialCrossCor | Expression correlation between cells of group A expressing... |
| plotNetwork | Plot an adjacency weight matrix as a network Adapted from... |
| plotNetwork3D | Plot an adjacency weight matrix as a network in 3D |
| purkinje | SlideSeq data of the Purkinje layer of the mouse cerebellum... |
| receptorLigandInfo | Receptor ligand list |
| rotatePos | Rotate position by angle theta in radians |
| signedLisa | Signed local indicators of spatial association to identify... |
| signedLisaPlot | Signed LISA plot |
| spatialCrossCor | Calculates spatial cross correlation for two features |
| spatialCrossCorMatrix | Calculates a spatial cross correlation for all pairs |
| spatialCrossCorTest | Tests for significance of spatial cross correlation for two... |
| spatialCrossCorTorTest | Tests for significance of spatial cross correlation for two... |
| winsorize | Winsorize expression values to prevent outliers |
