Manual cell selection in single cell transcriptomics using scSELpy supports the analysis of immune cell subsets.

ABSTRACT:

Introduction

Single cell RNA sequencing plays an increasing and indispensable role in immunological research such as in the field of inflammatory bowel diseases (IBD). Professional pipelines are complex, but tools for the manual selection and further downstream analysis of single cell populations are missing so far.

Methods

We developed a tool called scSELpy, which can easily be integrated into Scanpy-based pipelines, allowing the manual selection of cells on single cell transcriptomic datasets by drawing polygons on various data representations. The tool further supports the downstream analysis of the selected cells and the plotting of results.

Results

Taking advantage of two previously published single cell RNA sequencing datasets we show that this tool is useful fo

SUBMITTER: Dedden M 

PROVIDER: S-EPMC10166880 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature