Application note: TDbasedUFE and TDbasedUFEadv: bioconductor packages to perform tensor decomposition based unsupervised feature extraction.

ABSTRACT:

Motivation

Tensor decomposition (TD)-based unsupervised feature extraction (FE) has proven effective for a wide range of bioinformatics applications ranging from biomarker identification to the identification of disease-causing genes and drug repositioning. However, TD-based unsupervised FE failed to gain widespread acceptance due to the lack of user-friendly tools for non-experts.

Results

We developed two bioconductor packages-TDbasedUFE and TDbasedUFEadv-that enable researchers unfamiliar with TD to utilize TD-based unsupervised FE. The packages facilitate the identification of differentially expressed genes and multiomics analysis. TDbasedUFE was found to outperform two state-of-the-art methods, such as DESeq2 and DIABLO.

Availability and implementation

TDbasedUFE

SUBMITTER: Taguchi YH 

PROVIDER: S-EPMC10503044 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature