The MathIOmica Toolbox: General Analysis Utilities for Dynamic Omics Datasets.

The MathIOmica Toolbox: General Analysis Utilities for Dynamic Omics Datasets. Curr Protoc Bioinformatics. 2020 Mar;69(1):e91 Authors: Mias GI, Zheng M Abstract MathIOmica is a package for bioinformatics, written in the Wolfram language, that provides multiple utilities to facilitate the analysis of longitudinal data generated from omics experiments, including transcriptomics, proteomics, and metabolomics data, as well as any generalized time series. MathIOmica uses Mathematica's notebook interface, wherein users can import longitudinal datasets, carry out quality control and normalization, generate time series, and classify temporal trends. MathIOmica provides spectral methods based on periodograms and autocorrelations for automatically detecting classes of temporal behavior and allowing the user to visualize collective temporal behavior, and also assess biological significance through Gene Ontology and pathway enrichment analyses. MathIOmica's time-series classification methods address common issues including missing data and uneven sampling in measurements. As such, the software is ideally suited for the analysis of experimental data from individualized profiling of subjects, can facilitate analysis of data from the emerging field of individualized health monitoring, and can detect temporal trends that may be associated with adverse health events. In this article, we import a transcriptomics (RNA-sequencing) dataset collected ov...
Source: Current Protocols in Bioinformatics - Category: Bioinformatics Tags: Curr Protoc Bioinformatics Source Type: research