Cell type-specific Interaction Analysis using Doublets in scRNA-seq (CIcADA).

ABSTRACT:

Motivation

Doublets are usually considered an unwanted artifact of single-cell RNA-sequencing (scRNA-seq) and are only identified in datasets for the sake of removal. However, if cells have a juxtacrine attachment to one another in situ and maintain this association through an scRNA-seq processing pipeline that only partially dissociates the tissue, these doublets can provide meaningful biological information regarding the interactions and cell processes occurring in the analyzed tissue. This is especially true for cases such as the immune compartment of the tumor microenvironment, where the frequency and type of immune cell juxtacrine interactions can be a prognostic indicator.

Results

We developed Cell type-specific Interaction Analysis using Doublets in scRNA-seq (CIcADA)

SUBMITTER: Schiebout C 

PROVIDER: S-EPMC9949061 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature