Man pages for PolinaPavlovich/CONCLUS
ScRNA-seq workflow CONCLUS - from CONsensus CLUSters to a meaningful CONCLUSion.

calculateClustersSimilarityHaving cells similarity, calculate clusters similarity.
choosePaletteChoose palette for a plot.
clusterCellsInternalCluster cells and get similarity matrix of cells.
exportMatrixExport matrix to a file.
generateTSNECoordinatesGenerate and save t-SNE coordinates with selected parameters.
getGenesInfoCollect genes information to one table.
getMarkerGenesGet top N marker genes from each cluster.
initialisePathCreate all needed directories for CONCLUS output.
plotCellHeatmapSave markers heatmap.
plotCellSimilaritySave a cells similarity matrix.
plotClusteredTSNEPlot t-SNE. Addtionally, it can highlight clusters or states.
plotClustersSimilaritySave a similarity cluster matrix.
rankGenesRank marker genes by statistical significance.
runClusteringDBSCAN clustering on t-SNE results.
runCONCLUSRun CONCLUS in one click
runDBSCANRun clustering iterations with selected parameters using...
saveGenesInfoSave gene information into a table or tables for multiple...
saveMarkersListsSave top N marker genes for each cluster into a format...
testClusteringTo check one iteration of clustering before running full...
PolinaPavlovich/CONCLUS documentation built on May 10, 2019, 2:42 p.m.