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.
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
filterMethod filter for spaceST class.
heatmapsVisualize spatial heatmaps
mergeMerge and filter expression datasets
NormalizespaceSTMethod NormalizespaceST ST data.
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
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_clustersCalculate clusters based on topics.
topic.clustersMethod topic.clusters.
topic_computeHelper function to compute lda using cellTree package.
topic_heatmapPlot heatmap of lda results.
var.genesDetect variable genes using trendsceek package
volcano_plot_spaceSTVolcano plot
ludvigla/spaceST documentation built on May 6, 2018, 9:47 p.m.