Man pages for JEFworks/MERingue
Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with non-uniform cellular densities

BCLSpatial transcriptomics transcriptomics of 4 breast cancer...
cleanCountsFilter a counts matrix
drosophilaDrosophila embryo aligned ISH from the in situ database...
filterSpatialPatternsFilter for spatial patterns
getBnnNearest background neighbor
getClustersGet transcriptional clusters by graph-based clustering
getCrossLayerNeighborsNearest neighbors across layers
getDifferentialGenesDifferential expression analysis (adapted from PAGODA2)
getInterCellTypeWeightFilter adjacency weight matrix to between two subsets of...
getKnnK nearest neighbors
getMnnMutual nearest neighbors
getOverdispersedGenesGet overdispersed genes whose expression variance is higher...
getPvHelper function to get p-value from value and distribution...
getSpatiallyInformedClustersGet spatially informed clusters by weighting graph-based...
getSpatialNeighborsAdjacency weight matrix by Delaunay triangulations in 2D or...
getSpatialPatternsIdentify spatial clusters
groupSigSpatialPatternsGroup significant spatial patterns
interCellTypeSpatialCrossCorTests for inter-cell-type spatial cross-correlation between...
interpolateGridded bivariate interpolation For interpolating primary...
lisaTestLocal indicators of spatial association
makeAppMake a shiny app to interactively explore data
MERINGUEMERINGUE
mOBSpatial transcriptomics transcriptomics of the mouse...
moranPermutationTestDerive Moran's I p-value using permutation testing
moranTestSpatialy autocorrelation by Moran's I in C++
moranTest_DEPRECATEDSpatialy autocorrelation by Moran's I DEPRECATED! Use...
mouseCoronalVisium 10X Spatial Transcriptomics data of an adult mouse...
mPOAMERFISH data of the mouse pre-optic region for a female naive...
normalizeCountsNormalizes counts to CPM
plotEmbeddingPlot 2D embedding
plotInterCellTypeSpatialCrossCorExpression correlation between cells of group A expressing...
plotNetworkPlot an adjacency weight matrix as a network Adapted from...
plotNetwork3DPlot an adjacency weight matrix as a network in 3D
purkinjeSlideSeq data of the Purkinje layer of the mouse cerebellum...
receptorLigandInfoReceptor ligand list
rotatePosRotate position by angle theta in radians
signedLisaSigned local indicators of spatial association to identify...
signedLisaPlotSigned LISA plot
spatialCrossCorCalculates spatial cross correlation for two features
spatialCrossCorMatrixCalculates a spatial cross correlation for all pairs
spatialCrossCorTestTests for significance of spatial cross correlation for two...
spatialCrossCorTorTestTests for significance of spatial cross correlation for two...
winsorizeWinsorize expression values to prevent outliers
JEFworks/MERingue documentation built on June 11, 2022, 4:16 a.m.