Comprehensive Analysis of Large-Scale Transcriptomes from Multiple Cancer Types.

ABSTRACT: Various abnormalities of transcriptional regulation revealed by RNA sequencing (RNA-seq) have been reported in cancers. However, strategies to integrate multi-modal information from RNA-seq, which would help uncover more disease mechanisms, are still limited. Here, we present PipeOne, a cross-platform one-stop analysis workflow for large-scale transcriptome data. It was developed based on Nextflow, a reproducible workflow management system. PipeOne is composed of three modules, data processing and feature matrices construction, disease feature prioritization, and disease subtyping. It first integrates eight different tools to extract different information from RNA-seq data, and then used random forest algorithm to study and stratify patients according to evidences from multiple-modal infor

SUBMITTER: Nong B 

PROVIDER: S-EPMC8701385 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature