ABDS: tool suite for analyzing biologically diverse samples

Du, D.; Bhardwaj, S.; Parker, S. J.; Cheng, Z.; Zhang, Z.; Lu, Y.; Van Eyk, J. E.; Yu, G.; Clarke, R.; Herrington, D. M.; Wang, Y.

doi:10.1101/2023.07.05.547797

bioRxiv · 10.1101/2023.07.05.547797

ABDS: tool suite for analyzing biologically diverse samples

Du, D.·Bhardwaj, S.·Parker, S. J.·Cheng, Z.·Zhang, Z.·Lu, Y.·Van Eyk, J. E.·Yu, G.·Clarke, R.·Herrington, D. M.·Wang, Y.

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Abstract

MotivationAnalytics tools are essential to identify informative molecular features about different phenotypic groups. Among the most fundamental tasks are missing value imputation, signature gene detection, and expression pattern visualization. However, most commonly used analytics tools may be problematic for characterizing biologically diverse samples when either signature genes possess uneven missing rates across different groups yet involving complex missing mechanisms, or multiple biological groups are simultaneously compared and visualized. ResultsWe develop ABDS tool suite tailored specifically to analyzing biologically diverse samples. Mechanism-integrated group-wise imputation is developed to recruit signature genes involving informative missingness, cosine-based one-sample test is extended to detect enumerated signature genes, and unified heatmap is designed to comparably display complex expression patterns. We discuss the methodological principles and demonstrate the conceptual advantages of the three software tools. We also showcase the biomedical applications of these individual tools. Implemented in open-source R scripts, ABDS tool suite complements rather than replaces the existing tools and will allow biologists to more accurately detect interpretable molecular signals among diverse phenotypic samples. Availability and implementationThe R Scripts of ABDS tool suite is freely available at https://github.com/niccolodpdu/ABDS. Contactyuewang@vt.edu Supplementary informationSupplementary materials are available at Bioinformatics Advances online.

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Du, D., Bhardwaj, S., Parker, S. J., Cheng, Z., Zhang, Z., Lu, Y., Van Eyk, J. E., Yu, G., Clarke, R., Herrington, D. M., Wang, Y.. 2023-07-05. ABDS: tool suite for analyzing biologically diverse samples. https://doi.org/10.1101/2023.07.05.547797

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