Unveiling the immune microenvironment of complex tissues and tumors in transcriptomics through a deconvolution approach.

ABSTRACT: Accurately resolving the composition of tumor-infiltrating leukocytes is pivotal for advancing cancer immunotherapy strategies. Despite the success of some clinical trials, applying these strategies remains limited due to the challenges in deciphering the immune microenvironment. In this study, we developed a streamlined, two-step workflow to address the complexity of bioinformatics processes involved in analyzing immune cell composition from transcriptomics data. Our dockerized toolkit, DOCexpress_fastqc, integrates the hisat2-stringtie pipeline with customized scripts within Galaxy/Docker environments, facilitating RNA sequencing (RNA-seq) gene expression profiling. The output from DOCexpress_fastqc is seamlessly formatted with mySORT, a web application that employs a deconvolution algor

SUBMITTER: Chen SH 

PROVIDER: S-EPMC12044707 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature