Introduction

wombat-p pipelines is a bioinformatics analysis pipeline that bundles different workflow for the analysis of label-free proteomics data with the purpose of comparison and benchmarking. It allows using files from the proteomics metadata standard SDRF.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses ...

Joint multi-omics dimensionality reduction approaches for CAKUT data using peptidome and proteome data

Brief description In (Cantini et al. 2020), Cantini et al. evaluated 9 representative joint dimensionality reduction (jDR) methods for multi-omics integration and analysis and . The methods are Regularized Generalized Canonical Correlation Analysis (RGCCA), Multiple co-inertia analysis (MCIA), Multi-Omics Factor Analysis (MOFA), Multi-Study Factor Analysis (MSFA), iCluster, Integrative NMF ...

In this analysis, we created an extended pathway, using the WikiPathways repository (Version 20210110) and the three -omics datasets. For this, each of the three -omics datasets was first analyzed to identify differentially expressed elements, and pathways associated with the significant miRNA-protein links were detected. A miRNA-protein link is deemed significant, and may possibly be implying causality, if both a miRNA and its target are significantly differentially expressed.

The peptidome and ...

ORSON combine state-of-the-art tools for annotation processes within a Nextflow pipeline: sequence similarity search (PLAST, BLAST or Diamond), functional annotation retrieval (BeeDeeM) and functional prediction (InterProScan). When required, BUSCO completness evaluation and eggNOG Orthogroup annotation can be activated. While ORSON results can be analyzed through the command-line, it also offers the possibility to be compatible with BlastViewer or Blast2GO graphical tools.