Man pages for xmc811/Scillus
Scillus is a wrapper package enhancing the visualization of single cell omics data

add_program_scoreAdd gene program scores
analyze_mergedStreamlined analysis of Seurat object after integration
convert_symbolConversion between mouse and human gene symbols
exhaust_genesT cell exhaustion genes
filter_scdataFilter Seurat object
filter_scdata_listFilter Seurat object list
find_diff_genesFind differential expressed genes between two groups in each...
gene_in_dataTest whether a gene waas in the dataset
get_colorsGet a vector of colors
get_gene_dataObtain the expression data for genes
get_meta_dataObtain the meta data for features
get_paletteGet a vector of colors for cluster coding
get_spectrumGet a vector of colors for sample coding
get_top_genesGet top genes of each cluster
load_scfileLoad single cell RNA-seq data from directory or file
mm_hsMouse Human gene symbol lookup table
pathways.hallmarkHallmark genes
plot_all_cluster_goplot the GO enrichment analysis of all clusters of a dataset
plot_cluster_goplot the GO enrichment analysis of a cluster
plot_GSEAplot the results of GSEA
plot_GSVAplot the GSVA scores of given gene signatures
plot_heatmapPlot the heatmap of single cell dataset
plot_measureBox plot/Violin plot of gene expressions or meta measures
plot_measure_clusterSingle cell visualization - gene expression levels
plot_qcPlot the QC metrics of an individual biological sample
plot_scdataSingle cell visualization - merged and colored by biological...
plot_statPlot the basic statistics after cell clustering and labeling
rename_clusterRename clusters in Seurat object
test_GSEAGSEA analysis of differential gene expression in each cluster
vlookupLook up corresponding values from a lookup table
xmc811/Scillus documentation built on Nov. 5, 2019, 12:30 p.m.