Localized Marker Detector

Localized Marker Detector (LMD) is a computational framework designed for the identification of gene expression markers localized to specific cell populations within single-cell RNA sequencing data. The major workflow of LMD comprises the following three main steps:

  • Step1. Constructing a cell-cell affinity graph
  • Step2. Diffusing the gene expression value across the cell graph
  • Step3. Assigning a score to each gene based on the dynamics of its diffusion process
  • Optional Downstream tasks
    • Identifying gene modules and characterizing functional cell groups
    • Cross-sample comparison

Installation

LMD can be installed in R as follows:

install.packages("devtools")
devtools::install_github("KlugerLab/LocalizedMarkerDetector")

library("LocalizedMarkerDetector")

Example tutorial

Please check LMD tutorial.

References

References of LMD functions can be found here.