Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Provides a suite for trans-omics approaches. ECOMICS is composed of four components: (i) E-class, for taxonomic classification of prokaryotic and eukaryotic DNA sequences, (ii) FT2B to process nuclear magnetic resonance (NMR) spectra for downstream chemical analyses, (iii) Bm-Char which perform an assignment of specific compounds in lignocellulose, and (iv) HetMap to identify and visualize heterogeneous data and correlation matrices.
Provides an application for robust integration of heterogeneous data with orthogonal partial least squares (O2PLS). OmicsPLS offers a method and visualization tools to facilitate the development of advanced methodology. It includes functions to determine the number of components, fit, and inspect results. A memory-efficient implementation is used for high-dimensional data.
Allows general decomposition of variation for the integrated analysis of datasets. JIVE decomposes a dataset into a low-rank approximation capturing joint structure between data types, low-rank approximations capturing structure individual to each data type, and residual noise. It is applicable to datasets with more than two data types and has a simple algebraic interpretation. A JIVE analysis of gene expression and micro-RNA (miRNA) data on Glioblastoma Multiforme tumor samples reveals gene–miRNA associations and provides characterization of tumor types.
Assists users in detecting active pathways. MILPs is a mixed integer linear programming model that identifies cellular differentially expressed pathways responding to external conditions or diseases by using the molecular network topology and gene expression information. This method classifies differentially expressed pathways that can give deep insights into underlying molecular mechanisms. Finally, it can ensure connectivity of the identified pathway.
Implements state-of-the-art ensemble methods for module network inference. Lemon-Tree is a “one-stop shop” software suite for module network inference based on previously validated algorithms. The software is able to associate co-expression modules to multiple “regulator” types (expression regulators, structural DNA variants, phenotypic states, etc.) by assigning each of those independently as regulators of a module. It was benchmarked using large-scale datasets of somatic copy-number alterations and gene expression levels measured in glioblastoma samples from The Cancer Genome Atlas (TCGA).
Integrates and analyzes large-scale gene expression and metabolite profile data sets along with diverse biological information such as biochemical pathways and Gene Ontology (GO) terms. Plant MetGenMAP is an analysis and visualization package for plant systems biology. The software consists of three functional components: data management, pathway browser, and data set analyzer. It can assist researchers to generate novel biological hypotheses and derive new conclusions from high-throughput omics data sets.