ABDS: a bioinformatics tool suite for analyzing biologically diverse samples.
Res Sq
; 2024 May 30.
Article
in En
| MEDLINE
| ID: mdl-38853832
ABSTRACT
Bioinformatics software tools are essential to identify informative molecular features that define different phenotypic sample groups. Among the most fundamental and interrelated tasks are missing value imputation, signature gene detection, and differential pattern visualization. However, many commonly used analytics tools can be problematic when handling biologically diverse samples if either informative missingness possess high missing rates with mixed missing mechanisms, or multiple sample groups are compared and visualized in parallel. We developed the ABDS tool suite specifically for analyzing biologically diverse samples. Collectively, a mechanism-integrated group-wise pre-imputation scheme is proposed to retain informative missingness associated with signature genes, a cosine-based one-sample test is extended to detect group-silenced signature genes, and a unified heatmap is designed to display multiple sample groups. We describe the methodological principles and demonstrate the effectiveness of three analytics tools under targeted scenarios, supported by comparative evaluations and biomedical showcases. As an open-source R package, ABDS tool suite complements rather than replaces existing tools and will allow biologists to more accurately detect interpretable molecular signals among phenotypically diverse sample groups.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Language:
En
Journal:
Res Sq
Year:
2024
Document type:
Article
Affiliation country:
United States
Country of publication:
United States