Man pages for NCBI-Hackathons/clustifyR
Classification of Cell Types in Single-Cell RNA Sequencing Data

average_clustersAverage expression values per cluster
binarize_exprBinarize scRNA seq data
clustifyMain function to compare scRNA-seq data to bulk RNA-seq data.
clustifyr_methodsCorrelation functions available in clustifyR
compare_listscalculate adjusted p-values for hypergeometric test of gene...
cosineCosine distance
get_best_strFunction to make call and attach score
get_common_elementsFind entries shared in all vectors
getPCAGenesReturns a list of variable genes based on PCA
get_vargenesgenerate variable gene list from marker matrix
importance_heatmapHeatmap of average expression of most predictive genes across...
kl_divergenceKL divergence
matrixize_markersconvert candidate genes list into matrix
pbmc4k_avgMatrix of average gene expression per cluster from...
pbmc4k_markersMarker genes identified by Seurat from single-cell RNA-seq...
pbmc4k_markers_M3DropMarker genes identified by M3Drop from single-cell RNA-seq...
pbmc4k_matrixMatrix of single-cell RNA-seq PBMCs.
pbmc4k_metaMeta-data for single-cell RNA-seq PBMCs.
pbmc4k_vargenesvariable genes identified by Seurat from single-cell RNA-seq...
pbmc5_markersMarker genes identified by Seurat from single-cell RNA-seq...
pbmc5_matrixMatrix of single-cell RNA-seq PBMCs from 5'end kit.
pbmc5_metaMeta-data for single-cell RNA-seq PBMCs from 5'end kit.
pbmc_bulk_matrixBulk RNA-Seq data from sorted populations isolated from...
pbmc_pcaVariable genes defined by Principal components analysis of...
percent_clustersPercentage detected per cluster
plot_callPlot called clusters on a tSNE
plot_corPlot similarity measures on a tSNE
plot_genePlot gene expression on to tSNE
plot_tsnePlot a tSNE colored by feature.
pretty_paletteColor palette for plotting continous variables
reduce_expr_matrixReduce expression matrix to variable genes and binarize.
refine_clustersRefine clustering using reference data
run_gseaRun GSEA to compare a gene list(s) to per cell or per cluster...
use_seurat_compFunction to convert labelled seurat object to avg expression...
vector_similarityCompute similarity between two vectors
NCBI-Hackathons/clustifyR documentation built on Sept. 30, 2018, 9:58 a.m.