TABLE 1.
A complied list of various resources for supporting FAIR and interactive multi-omics study.
| Serial No | Tools | Purpose | Link | References (if any) |
| Popular/Emerging Multi-omics Tools | ||||
| 1 | mixOmics | A tool with a framework that provides wide range of multivariate statistical methods for exploratory data analysis (EDA). This involves features identification, extraction and selection. | http://mixomics.org/ | Rohart et al., 2017 |
| 2 | MOFA | A probabilistic multi-omics factor analysis-based framework that involves EDA and data integration. (Unsupervised) | https://github.com/bioFAM/MOFA | Argelaguet et al., 2018 |
| 3 | SNF | A multi-view network and fusion analysis framework for feature extraction, pairwise similarity, clustering, classification, etc. | https://cran.r-project.org/web/packages/SNFtool/index.html | Wang et al., 2014 |
| 4 | miodin | A multi-level statistical framework involving vertical and horizontal integration of multi-omics data. | https://algoromics.gitlab.io/miodin/ | Ulfenborg, 2019 |
| 5 | Paintomics | A web-based systems biology tool for multi-omic integration and visualization across multi-species. | www.paintomics.org | Hernández-de-Diego et al., 2018 |
| 6 | 3Omics | A web-based application for integration and analysis of multi-omics data. | https://3omics.cmdm.tw/ | Kuo et al., 2013 |
| Data Sharing | ||||
| 1 | OmicsDI | An aggregated database facilitating the discovery of heterogenous published omics datasets across studies. | http://www.omicsdi.org | Perez-Riverol et al., 2017 |
| 2 | Zenodo | A general-purpose open-access data, softwares, etc repository that allows user to obtain a citable DOI. | https://zenodo.org/ | NA |
| 3 | OSF | An open platform to enable collaboration by registering research projects, materials, data and documentation. | https://osf.io/ | NA |
| Code Sharing | ||||
| 1 | GitHub | A version-controlled code sharing and collaborative platform. | https://github.com/ | NA |
| 2 | BitBucket | https://bitbucket.org/ | NA | |
| 3 | GitLab | https://about.gitlab.com/ | NA | |
| Workflow Sharing | ||||
| 1 | Common Workflow Language (CWL) | An open standard for describing analysis workflows which makes them portable and scalable across a variety of software and hardware environments. | https://www.commonwl.org/ | Amstutz et al., 2016 |
| 2 | Nextflow | An enterprise level workflow language for writing scalable and reproducible scientific pipelines. | https://www.nextflow.io/ | Di Tommaso et al., 2017 |
| 3 | Snakemake | A workflow language for writing scalable and reproducible scientific pipelines. | https://snakemake.readthedocs.io/en/stable/ | Koster and Rahmann, 2012 |
| Environment Sharing | ||||
| 1 | Conda | A package manager and computation environment management system. | https://docs.conda.io/en/latest/ | NA |
| 2 | Bioconda | A channel for the conda package manager specializing in bioinformatics software. | https://bioconda.github.io/ | Grüning et al., 2018 |
| 3 | Docker | A container platform that provided OS-level virtualization for providing reproducible computation environment. | https://www.docker.com/ | NA |
| 4 | BioContainers | A community-driven project that provides docker based containerized bioinformatics software. | https://biocontainers.pro/ | da Veiga Leprevost et al., 2017 |
| 5 | renv | A R-package that helps create reproducible environments for R-based projects. | https://rstudio.github.io/renv/ | NA |
| Serial No | Tools | Purpose | Link | References (if any) |
| Data Visualization | ||||
| 1 | Shiny | A framework in R for doing GUI based interactive applications. | https://shiny.rstudio.com/ | NA |
| 2 | Plotly | A cross language interactive plot library. | https://plotly.com/ | NA |
| 3 | bokeh | A Python library for Interactive data visualization in browser. | https://bokeh.org/ | NA |
| 4 | D3,js | A JavaScript library for producing dynamic, interactive data visualizations in web browsers. | https://d3js.org/ | NA |
| 5 | Cytoscape | A platform for network data integration, analysis, and visualization. | https://cytoscape.org/ | NA |