EURYALE is a Nextflow pipeline designed for the sensitive taxonomic classification and flexible functional annotation of metagenomic shotgun sequences. It provides a comprehensive solution for preprocessing, assembly, alignment, taxonomic classification, and functional annotation of metagenomic data. EURYALE builds upon the Snakemake-based pipeline MEDUSA. EURYALE inherits the tools present in MEDUSA, selected based on rigorous benchmarks for performance, accuracy, and sensitivity. The new pipeline has been developed with the nf-core pipeline template, which focuses on modularity, allowing a high degree of parameterization. EURYALE provides easier resource management, enforcing strict memory and CPU requirements based on its Nextflow configuration. It has also become more versatile, as it can be executed using Docker and Singularity, which further extends its usability across various platforms. It can also natively take advantage of computational infrastructures such as SLURM and Amazon Web Services. EURYALE inherits the sensitivity in taxonomic classification and flexibility in functional annotation of its predecessor, combined with improved versatility.

MOTIVATION: Dendrogram is a classical diagram for visualizing binary trees. Although efficient to represent hierarchical relations, it provides limited space for displaying information on the leaf elements, especially for large trees. RESULTS: Here, we present TreeAndLeaf, an R/Bioconductor package that implements a hybrid layout strategy to represent tree diagrams with focus on the leaves. The TreeAndLeaf package combines force-directed graph and tree layout algorithms using a single visualization system, allowing projection of multiple layers of information onto a graph-tree diagram. The Supplementary Information provides two case studies that use breast cancer data from epidemiological and experimental studies. AVAILABILITY AND IMPLEMENTATION: TreeAndLeaf is written in the R language, and is available from the Bioconductor project at http://bioconductor.org/packages/TreeAndLeaf/ (version≥1.4.2). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: Several freely available tools perform analysis using algorithms developed to identify significant variation of gene expression individually. The transcriptogramer R package uses protein-protein interaction to perform differential expression of functionally associated genes. The software assesses expression profile of entire genetic systems and reveals which biological systems are significantly altered in case-control designed transcriptome experiments. RESULTS: R/Bioconductor transcriptogramer package projects expression values on an ordered gene list to perform topological analysis, differential expression and gene ontology enrichment analysis, independently of data platform or operating system. AVAILABILITY AND IMPLEMENTATION: http://bioconductor.org/packages/transcriptogramer. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

UNLABELLED: ViaComplex is an open-source application that builds landscape maps of gene expression networks. The motivation for this software comes from two previous publications (Nucleic Acids Res., 35, 1859-1867, 2007; Nucleic Acids Res., 36, 6269-6283, 2008). The first article presents a network-based model of genome stability pathways where we defined a set of genes that characterizes each genetic system. In the second article we analyzed this model by projecting functional information from several experiments onto the gene network topology. In order to systematize the methods developed in these articles, ViaComplex provides tools that may help potential users to assess different high-throughput experiments in the context of six core genome maintenance mechanisms. This model illustrates how different gene networks can be analyzed by the same algorithm. AVAILABILITY: (http://lief.if.ufrgs.br/pub/biosoftwares/viacomplex).