ScAmpi-A versatile pipeline for single-cell RNA-seq analysis from basics to clinics.

ABSTRACT: Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique to decipher tissue composition at the single-cell level and to inform on disease mechanisms, tumor heterogeneity, and the state of the immune microenvironment. Although multiple methods for the computational analysis of scRNA-seq data exist, their application in a clinical setting demands standardized and reproducible workflows, targeted to extract, condense, and display the clinically relevant information. To this end, we designed scAmpi (Single Cell Analysis mRNA pipeline), a workflow that facilitates scRNA-seq analysis from raw read processing to informing on sample composition, clinically relevant gene and pathway alterations, and in silico identification of personalized candidate drug treatments. We demonstrate

SUBMITTER: Bertolini A 

PROVIDER: S-EPMC9200350 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature