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 |
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