Table 2.
Meta-omics tools that contribute to network construction.
| Network | Tool | Yeara | Description | Output | Data |
|---|---|---|---|---|---|
| Co-occurrence network | UPARSE [70] | 2013 | An approach using UPARSE-OTU algorithms for producing clusters | OTUs in the community | Metagenomics |
| MetaPhlan2 [71] | 2015 | A tool for profiling composition of communities relying on unique clade-specific marker genes | Species in the community and their relative abundance | ||
| mOTUs2 [72] | 2019 | An approach based on marker gene OTUs that quantifies microbial species in metagenomic samples | Taxonomic assignment, relative abundance | ||
| MicroPro [73] | 2019 | A pipeline integrated reference-based methods with de novo assembly-based methods for microbial abundance from whole-genome sequencing | Reference-based known and assembly-binning-based unknown microbial abundance table | ||
| QIIME2 [69] | 2019 | An updated pipeline for demultiplexing and quality filtering, OTU picking, taxonomic assignment, phylogenetic reconstruction, visualizations | OTU table; taxonomy assignment based on reference | ||
| Genome-scale metabolic network | MetaQUBIC [74] | 2019 | An integrated biclustering-based pipeline for gene module detection that integrates both metagenomic and metatranscriptomic data | Functional enriched gene modules | Multi-omics |
| MetaTrans [75] | 2016 | A pipeline to analyse the structure and functions of active microbial communities from RNA-Seq data | Taxonomical abundance, functional assignment | Metatranscriptomics | |
| Co-occurrence network and genome-scale metabolic network | SAMSA [76] | 2016 | A pipeline for the analysis of gut microbiome data, focusing either on organism-specific activity or functional activity within sample | Organism abundance, RNA organism taxonomy list, function counts | |
| MG-RAST [77] | 2008 | A pipeline producing functional assignments of sequences in metagenome by comparing protein and nucleotide databases | Metabolic reconstruction and composition of the sample | Metagenomics/metatranscriptomics | |
| HUMAnN2 [78] | 2018 | A pipeline for profiling presence or absence and abundance of microbial pathways in a community from DNA/RNA reads | Species abundance and species-level metabolic pathway abundance in the community | ||
| PPI network | IdentiPy [79] | 2018 | A Python-based extensible engine peptide identification, postsearch validation, protein inference and quantification | Quantitative protein list | Metaproteomics |
| Trans-Proteomic Pipeline [80] | 2010 | A robust open-source standardized data processing pipeline for large-scale reproducible quantitative MS proteomics | Protein groups that sorted in descending order by probability | ||
| compleXView [81] | 2017 | A webserver that calculates measures of abundance, reproducibility and specificity to infer PPI | The PPI table | ||
| Metabolomics-driven metabolic network | Pathos [82] | 2011 | A webserver that analyses mass spectrometric data and displays metabolites and metabolic pathways | Metabolites and abundance changes, metabolic pathways | Metabolomics |
| MetaboAnalyst [83] | 2018 | A webserver for comprehensive metabolomic data analysis, interpretation and integration with other omics data | Biomarker identification, an MS peaks to pathways module | ||
| Netome [84] | 2018 | A tool for processing and analysing metabolomics data and exploring associations with other omics data and metadata | Metabolite abundances, testing association such as microbes and metabolites |
aPublication year.