SciGeneX: enhancing transcriptional analysis through gene module detection in single-cell and spatial transcriptomics data.

ABSTRACT: The standard pipeline to analyze single-cell RNA-seq or spatial transcriptomics data focuses on a gene-centric approach that overlooks the collective behavior of genes. However, understanding cell populations necessitates recognizing intricate combinations of activated and repressed pathways. Therefore, a broader view of gene behavior offers more accurate insights into cellular heterogeneity in single-cell or spatial transcriptomics data. Here, we describe SciGeneX (Single-cell informative Gene eXplorer), a R package implementing a neighborhood analysis and a graph partitioning method to generate co-expression gene modules. These modules, whether shared or restricted to cell populations, collectively reflect cellular heterogeneity. Their combinations are able to highlight specific cell pop

SUBMITTER: Bavais J 

PROVIDER: S-EPMC12004220 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature