Package index • iTALK

Core Functions

Main functions for cell-cell communication analysis

rawParse(): Parsing the data to get top expressed genes

FindLR(): Finding ligand-receptor pairs

DEG(): Call DEGenes

database: Ligand-Receptor Interaction Database

Differential Expression Methods

Statistical methods for identifying DEGs

WilcoxTest(): Differential expression using wilcox

DESeq2Test(): Differential expression using DESeq2

edgeRTest(): Differential expression using edgeR

MASTTest(): Differential expression using MAST

MonocleTest(): Differential expression using monocle

SCDETest(): Differential expression using scde

DESingleTest(): Differential expression using DEsingle

Visualization

Functions for visualizing cell communication

LRPlot(): Plotting ligand-receptor pairs

NetView(): Network Viewing of cell-cell communication

TimePlot(): Plotting ligand-receptor pairs

Species Conversion

Cross-species gene conversion utilities

detect_species(): Detect Species from Gene Names

convert_species_biomart(): Convert Genes Between Species Using BioMart

convert_expression_matrix(): Convert Expression Matrix Between Species

convert_data_species(): Apply Species Conversion to iTALK Data Frame

species_conversion: Species Conversion System for iTALK