Man pages for ludvigla/ST_analysis3D

align.gridsAlign grid using shiny app
batch.correctBatch correction of spaceST data
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
convert_coordinates_from_jsonConvert coordinates produced from json
ensembl2hgncConvert from ENSEMBL ID to HGNC symbol
format_3D_dataUsed to format 3D data
get_coordinatesObtain coordinates from expression data list of expression...
get.spaceSTFilter ST expression data.
get.xCellBootBootstrap xCell data.
initialize-xCellBoot-methodInitialize values for xCellBoot object.
interpolate_2D_dataInterpolate object values over "cell population"
jet.colorsJet colorscale
js3DscatterCreate interactive scatterplot3js
manipulate.gridScale, move and rotate binary dot pattern
median.bootstraps-xCellBoot-methodExtract median bootstrap values
merge_exp_listMerge and filter expression datasets
morph.3dPlot interactive 3D scatter
pca_plotpca of expression data
pca.spaceSTPlot pca of spaceST data
plot.QC.spaceSTPlot unique genes per feature and transcripts per feature
rasterize_scatterrasterize scatter data from HE image
rename_listRename rownames of lists
scale2rangeScale to custom range
scatter_HETest settings for interpolation
spaceST-classAn S4 class to obtain filtered ST data for 3D analysis.
spatial.clustersVisualize spatial distribution of clusters
spatial.heatmapVisualize spatial heatmaps
spatial.tSNEPlot t-SNE and visualize clusters
ST_statisticsQuality Control statistics
ST_statistics.plotQuality Control plot
subset.xCellCalculate xCell scores for cluster matrix
topic_cluster_matrixCompute cluster matrix
topic_cluster_QC_plotQA plot for pooled data
topic_clustersCalculate clusters based on topics
topic_computeHelper function to compute lda using cellTree package
topic_heatmapPlot heatmap of lda results
violin.bootstrapsViolin plot of xCell scores
xCellBoot-classAn S4 class to obtain filtered ST data for 3D analysis.
xCell.bootstrapBootstrap function for xCell
xCell.heatmapxCell heatmap
ludvigla/ST_analysis3D documentation built on Sept. 16, 2017, 7:25 p.m.