Welcome to MultiOmicsIntegrator documentation!

MOI is a nextflow pipeline that aims to cover extensive and diverse omics analyses. MOI offers end-to-end analysis of RNAseq, taking into account different RNA molecules, like isoforms of genes and miRNAs. In addition to traditional RNAseq pipelines, MOI has tools for functional annotation and secondary structure prediction of RNA transcripts. Moreover, it can cover proteomics and metabolomics analyses. For the latter, MOI has additional tools for accessing differences in specific biochemical attributes. All available omics-specific workflows can run autonomously, however, if the user wishes they can integrate their data either with data driven or biology driven approaches. Finally, differentiating from existing pipelines we offer biotranslator as our pathway enrichment algorithm as it can better mitigate the high noise inhereit with biological data as well as omnipathr for advance downstream analyses.

Note

This project is additional documentation for MOI: MultiOmicsIntegrator: an integrated solution for omics analyses.

General inputs and outputs

The MOI pipeline is organized into individual modules, each responsible for a specific step in the analysis workflow. The modular design facilitates code flexibility in incorporating new analyses techniques or custom implementations, as well as easy maintenance and scalability.

MOI’s behavior is regulated through the params.yml files, each named to align with the specific analysis segment they govern. In those files the user is tasked with specifying input and output parameters and with the optional fine-tuning intricacies such as algorithm selection and algorithmic configurations.

The pipeline’s inputs are streamlined to one csv file. This file accommodates either a solitary column of SRA codes or a directory pointing to the location of fastq files, along with any other metadata pertaining to their samples. If the analysis commences with count (abundance) matrices the user can specify the directory of the this matrix along with a phenotype file.

MOI produces extensive outputs, including informative plots and intermediate results in the form of text and RData objects for each module, accommodating users who seek further utilization or detailed inspection of results. Outputs are organized hierarchically based on the user’s parameterization; for example, the pathway enrichment analysis of genes will be located under the directory “/user_defined_output_directory/genes/biotranslator/”.

Most important tools

Omics	Functionality	Tools
Genes, miRNA, isoforms	SRA download	SRA toolkit
Genes, miRNA, isoforms	Quality control	FastQC, trimgalore
Genes, miRNA, isoforms	Align and Assembly	Salmon, samtools, STAR, Hisat2, StringTie2
Genes, miRNA, isoforms, proteins, lipids	Data preprocessing	R packages: edger, limma, sva, ggplot2, ComplexHeatmap
Proteins, lipids	Specific for proteins and lipids	R packages: p reprocesscore, mstus normalization
Lipids	Specific for lipids	R packags: lipidr
Genes, miRNA, isoforms, proteins, lipids	Differential expression analyss	R packages: DESeq2, edger, RankProd, ggplot2 ComplexHeatmap
Genes, miRNA, isoforms, proteins, lipids	Correlation analysis	R package stats
Genes, miRNA, isoforms, proteins, lipids	Pathway enrichment analysis	Cl usterprofiler, Biotranslator
Lipids	Specific for lipids pathway enrichment analysis	Custom tool: Lipidb
Genes, miRNA, isoforms, proteins	RIDDER (module to identify IRE1 substrates)	gRIDD, RNAeval, fimo
Genes, miRNA, isoforms	Functional annotation	CPAT, signalP, pfam
Genes, miRNA, isoforms, proteins	Secondary structure prediction	RNAfold, RNAeval
Genes, miRNA, isoforms, proteins	Find motif	fimo
Isoforms	Genome wide isoform analysis	Isoform SwitchAnalyzer

Contents

• Installation
  • Pipeline summary
    • The pipeline can be found at:
    • Supplementary materials for this pipeline can be found at this zenodo repository:
  • Quick Start
    • In addition check/modify resources (in params_mcia.yml) according to your system:
  • Common issues:
  • Documentation
• Genes
  • Nessecary inputs
  • Important
  • Start from SRA
  • Reference files
  • Running the pipeline
    • Functionality
  • Note: All files need to be in the format:
  • Preprocess
  • DEA
    • Note
    • edger
    • DESeq2
    • Important note
    • RankProduct rankprod
  • PEA
• Isoforms
  • Necessary inputs
  • Important
  • Start from SRA
  • Reference files
  • Running the pipeline
  • Note: All files need to be in the format:
• miRNA
  • Necessary inputs
  • Important
  • Start from SRA
  • Reference files
  • Running the pipeline
    • Functionality
  • Note: All files need to be in the format:
  • Preprocess
  • DEA
    • Note
    • edgeR
    • DESeq2
    • Important note
    • rankprod
• Proteins
  • Necessary inputs
  • Important
  • Running the pipeline
    • Preprocess
      • Note
    • DEA
      • edger
      • DESeq2
      • Important note
      • RankProduct
    • Pathway Enrichment Analysis (PEA)
      • BIOTRANSLATOR
• Lipids
  • Necessary inputs
  • Important
  • Running the pipeline
  • Functionality
    • All in one analysis with LipidR
    • LipiDB
    • PEA
      • BIOTRANSLATOR
• Integration
  • Necessary inputs
    • Important
  • Running the pipeline
  • Functionality
    • LipiDB
    • multiMiR
    • Exploratory analysis
    • Correlation analysis
    • OmnipathR
    • Additional omics types
• MOI: Output
  • Introduction
  • Pipeline overview
  • RNAseq analysis
  • Isoform analysis
  • Lipidomics analysis
  • Integration
• Core Nextflow arguments
  • -profile
  • -resume
    • Custom configuration
  • Resource requests
  • Updating containers (advanced users)
  • nf-core/configs
    • Azure Resource Requests
    • Running in the background
    • Nextflow memory requirements