---
title: "Tools & Resources"
lang: ko
url: https://www.gereallife.com/ko/services/resources-tools.html
canonical: https://www.gereallife.com/ko/services/resources-tools.html
entity: Shanghai Gereallife Biotech Co., Ltd
updated: 2026-11-02
---
KEY POINTS 
 
- MetaboAnalyst online metabolomics analysis platform with statistics and pathway enrichment
- Galaxy open-source web platform supporting diverse omics workflows
- OmicsHub Gereallife's in-house cloud platform for interactive multi-omics reports 
 
 
 

## 01Public Databases

 

| Database | Type | Description | URL |
| --- | --- | --- | --- |
| HMDB | Metabolomics | human metabolome database with 220,000+ metabolite entries | hmdb.ca |
| KEGG | pathway database | metabolic, signaling and disease pathways | genome.jp/kegg |
| UniProt | protein database | protein sequences, functions and modifications | uniprot.org |
| MetaboLights | Metabolomics | repository of metabolomics raw data and metadata | ebi.ac.uk/metabolights |
| PRIDE | Proteomics | repository of proteomics MS data | ebi.ac.uk/pride |
| GEO / SRA | transcriptomics / genomics | public repository of gene-expression and sequencing data | ncbi.nlm.nih.gov/geo |
| STRING | protein interaction | protein–protein interaction network database | string-db.org |
| Reactome | pathway database | manually curated biological-pathway database | reactome.org |

 
 
 
 

## 02Analysis Software

 

### integrated platform

 
- MetaboAnalyst online metabolomics analysis platform with statistics and pathway enrichment
- Galaxy open-source web platform supporting diverse omics workflows
- OmicsHub Gereallife's in-house cloud platform for interactive multi-omics reports 

### R/Bioconductor packages

 
- edgeR / DESeq2 standard tool for transcriptome differential-expression analysis
- limma linear-model differential analysis for microarrays and RNA-seq
- clusterProfiler GO/KEGG enrichment analysis and visualization 

### multi-omics integration tools

 
- mixOmics / DIABLO multi-omics integration and classification modeling
- MOFA2 multi-modal factor analysis for co-variation patterns
- WGCNA weighted gene co-expression network analysis 
 
 
 

## 03Online Analysis Platforms

 

### Galaxy EU

European Galaxy server integrating 8,000+ bioinformatics tools with drag-and-drop workflow building.

### MetaboAnalyst

One-stop online metabolomics analysis covering data processing, statistical testing, pathway enrichment and visualization.

### iDEP

Interactive transcriptomics platform—differential analysis, clustering and enrichment in clicks.

 
 
 

## 04Learning Resources

 

### Tutorials

Bioconductor official tutorials, Galaxy Training Network, Coursera bioinformatics specializations

### Reference Books

《Bioinformatics Data Skills》、《Modern Statistics for Modern Biology》、《Computational Genomics with R》

### Journals

Nature Methods、Bioinformatics、Nucleic Acids Research、Briefings in Bioinformatics

### Open-Source Communities

Biostars Q&A community, SEQanswers forum, GitHub open-source projects

 
 
 

## 05Report Templates

 

### Standard transcriptomics report

QC report differential-gene list volcano plot heatmap GO/KEGG enrichment

### Standard proteomics report

identification statistics differential-protein list volcano plot PPI network Functional Annotation

### Standard metabolomics report

Metabolite Identification differential metabolites PLS-DA score plot pathway bubble chart

### Multi-omics integration report

cross-omics correlation analysis DIABLO model integrated network biological interpretation

 
 
 

## Q&AFAQ

 Is there one online tool that takes me from metabolomics data processing to pathway enrichment? its one-stop online analysis covers data processing, statistical testing, pathway enrichment and visualization. 
 Do I need to write code to run an RNA-seq workflow online? Not necessarily. Galaxy is an open-source web platform supporting diverse omics workflows, and the European Galaxy server integrates 8,000+ bioinformatics tools with drag-and-drop workflow building. 
 Which database should I check to see whether a metabolite belongs to a pathway? KEGG is a pathway database covering metabolic, signaling and disease pathways, while Reactome is a manually curated biological-pathway database. 
 After differential expression, what should I use for GO/KEGG enrichment? clusterProfiler handles GO/KEGG enrichment analysis and visualization; for the upstream step, edgeR / DESeq2 are the standard tools for transcriptome differential-expression analysis. 
 I have both metabolomics and proteomics data. What can integrate them into one model? mixOmics / DIABLO are used for multi-omics integration and classification modeling; if you only want co-variation patterns, MOFA2 performs multi-modal factor analysis. 
 
 
 
 
 
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 Contact the team → 
 
 
 
 

 
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