Man pages for ludvigla/spaceST
spaceST

batch.correctMethod batch.correct for spaceST class.
BuildTopicSNNBuild SNN graph
calc_cp10kCalculate cp10k
CalcSNNSparseFunction to convert the knn graph into the snn graph. Stored...
cluster_matrixCompute cluster matrix.
clusterSTCalculate clusters based on topics.
collect_gene_dataCollect data from bioMmRt
convertConvert from ENSEMBL ID to HGNC symbol or MGI symbol
coordinatesget_coordinates: obtain spatial coordinates
countsMethod counts.
CreatespaceSTobjectInitiialize and setup the spaceST object
DE_heatmapPlot DE heatmap
ExtractTopFeaturesSTExtract top features
filterMethod filter for spaceST class.
getLDAMethod topic.clusters.
heatmapsVisualize spatial heatmaps
LDAHelper function to compute lda using cellTree package.
mergeMerge and filter expression datasets
normcountsMethod normcounts.
palette.selectCreate palettes
plot_QC_spaceSTPlot unique genes per feature and transcripts per feature.
RunDEspaceSTRun DE analysis using the edgeR package to detect...
RunModularityClusteringspaceSTRuns the modularity optimizer java program...
RunTSNEspaceSTt-SNE of spaceST data
SetIfNullHelper function
smooth.vizSmooth visualization of gene expression patterns
spaceSTThe spaceST class.
spaceST-methodsspace-ST methods.
spaceST-packageThis package includes functions used to process, analyze and...
spaseST-methodsMethod show for spaceST class.
spatial.clustersVisualize spatial distribution of clusters.
SpatialNetworkspaceST network graphs
spots_under_tissueMethod spots_under_tissue for spaceST class.
spPCAMethod spPCA for spaceST class.
ST_statisticsQuality Control statistics
ST_statistics_plotQuality Control plot
tesselation.plotVoronoi tesselation plot
tessVizPlot tesselated object.
tiles2polygonConvert tiles and add color.
topic.clustersMethod topic.clusters.
topic_heatmapPlot heatmap of lda results.
var_genesDetect variable genes using trendsceek package
volcano_plot_spaceSTVolcano plot
ludvigla/spaceST documentation built on Aug. 18, 2018, 5:37 a.m.