CITMIC

CITMIC is a method for estimate cell infiltration score

Introduction

CITMIC can infer the cell infiltration of the TME by simultaneously measuring 86 different cell types, constructing an individualized cell-cell crosstalk network based on functional similarities between cells, and using only gene transcription data. This is a novel approach to estimate the relative cell infiltration levels, and which were shown to be superior to the current methods.

A notice on operating system compatibility

• We recommend using as input the gene expression matrix normalized by log2(fpkm+1).
• If your computer has multiple CPU cores, we recommend that you select the number of cl.cores to apply to CITMIC based on parallel::detectCores(). He will greatly improve the efficiency of the function's operation.
• R (≥ 4.2.0): We developed this R package using R version 4.3.x.

Installation

Install CITMIC using:

install.packages(c('devtools', 'BiocManager'))
remotes::install_github("zhaopapers/CITMIC")

Usage

Load the package using library(CITMIC). We provide a vignette for the package that can be called using: vignette("CITMIC"). Alternatively, you can view the online version on CRAN, The examples I provided would take several minutes to run on a normal desktop computer. Basically that is all you have to know.