Man pages for ludvigla/spaceST

addalphaAdd alpha to channel 4 in rgba space
align.gridsAlign grid using shiny app
batch.correctBatch correction of spaceST data
bias.bootstraps-xCellBoot-methodExtract bias data
BuildTopicSNNBuild SNN graph
CalcSNNSparseFunction to convert the knn graph into the snn graph. Stored...
cast2listCast merged data to list of matrixes
celltype.bootstraps-xCellBoot-methodExtract celltype bootstrap replicates
clust2featureRearrange xCell output from clusters to features
cluster.bootstraps-xCellBoot-methodExtract cluster bootstrap replicates
convertConvert from ENSEMBL ID to HGNC symbol
coordinatesget_coordinates: obtain spatial coordinates
CreatespaceSTobjectFilter ST expression data.
CreatexCellBootBootstrap xCell data.
format-3DUsed to format 3D data
interpolate_2D_dataInterpolate object values over "cell population"
js3DscatterCreate interactive scatterplot3js
manipulate.gridScale, move and rotate binary dot pattern
mean.bootstraps-xCellBoot-methodExtract mean bootstrap values
mergeMerge and filter expression datasets
morph-3DPlot interactive 3D scatter
normNormalize using CPTK method
normalizeNormalize ST data
obs.bootstraps-xCellBoot-methodExtract obserevd bootstrap values
pcaPlot pca of spaceST data
pca_plotpca of expression data
QCPlot unique genes per feature and transcripts per feature
rasterize_scatterrasterize scatter data from HE image
rename_listRename rownames of lists
RunModularityClusteringspaceSTRuns the modularity optimizer java program...
RunTSNEspaceSTt-SNE of spaceST data
scaleScale to custom range
scatter_HEGenerate binary dot pattern
SetIfNullHelper function
show-methodsshow method for spaceST
spaceSTThe spaceST class
spatial.clustersVisualize spatial distribution of clusters
spatial.heatmapVisualize spatial heatmaps
SpatialNetworkspaceST network graphs
ST_statisticsQuality Control statistics
ST_statistics.plotQuality Control plot
subset.xCellCalculate xCell scores for cluster matrix
topic_cluster_matrixCompute cluster matrix
topic_cluster_QC_plotQC plot for pooled data
topic_clustersCalculate clusters based on topics
topic_computeHelper function to compute lda using cellTree package TODO:...
topic_heatmapPlot heatmap of lda results
violin.bootstrapsViolin plot of xCell scores
xCellBootxCellBoot class
xCell.bootstrapBootstrap function for xCell
xCell.heatmapxCell heatmap
ludvigla/spaceST documentation built on Dec. 14, 2017, 12:58 p.m.