Help & Documentation
Learn how to use the Mini Omics Data Portal tools effectively
Quick Start
Getting Started
- 1. Choose a Species: Select your organism of interest from the homepage
- 2. Select a Tool: Choose from Genome Browser, Gene Browser, or BLAST Search
- 3. Explore Data: Use the interactive tools to analyze your data
Navigation Tips
- Use the species statistics to understand data scope
- Tab between tools without losing your work
- Use "Open in New Tab" for detailed analysis
- All tools can be opened in new windows for parallel work
Tool Guide
miniODP connects genome browsing, gene-centered exploration, and sequence search through three main tools.
Genome Browser
JBrowse 2
Interactive visualization of genomic features, annotations, and sequencing data.
Key Features:
- Genome navigation
- Track visualization
- Feature search
- Data export
Default Tracks:
- Ensembl gene models
- RNA-seq coverage
- ATAC-seq coverage
- ChIP-seq coverage
Usage Tips:
- Use track selector to search by categories, samples, or technologies
- Click track names to change display settings and colors
- Search genes by name, ID, or genomic coordinates
- Use 'Share' button to get links for current view
- Open in new tab for detailed analysis
Gene Browser
Dash
Interactive gene expression analysis and multi-omics data exploration. Search genes using the sidebar, then explore different data types through the tabs below.
Gene Info
Comprehensive gene annotation and metadata. View basic information including gene ID, name, description, genomic location, and sequence. Explore functional annotations from GO (Gene Ontology) and InterPro domains. For transcription factors, view family classification with links to AnimalTFDB. Find orthologous genes across different species with direct links to their pages.
- Gene sequences (DNA, CDS, protein)
- GO terms (BP, MF, CC)
- InterPro domain annotations
- Cross-species orthologs
BulkRNA
Visualize bulk RNA-seq expression data across multiple studies and conditions. Select from available studies, each containing multiple samples organized by tissue, developmental stage, or experimental condition. Expression values can be displayed as raw TPM, log-transformed, or z-score normalized for cross-gene comparison.
- Interactive heatmap visualization
- Multiple studies selection
- TPM / Log2 / Z-score transforms
- Export expression matrix as CSV
scRNA
Explore single-cell RNA-seq data with dimensionality reduction visualizations. View gene expression patterns on UMAP/tSNE embeddings, with cells colored by expression level. Use violin plots to compare expression distributions across cell clusters. Adjust the expression threshold to filter out low-signal noise and highlight cells with significant expression.
- UMAP/tSNE feature plots
- Cluster-based violin plots
- Expression threshold filtering
- Multiple colorscale options
scATAC
Visualize single-cell chromatin accessibility data. For each gene, view accessibility of associated regulatory peaks on UMAP embeddings. This helps identify cell populations with open chromatin at gene regulatory regions, complementing expression data from scRNA-seq.
- Peak accessibility on UMAP
- Gene-associated peak search
- Accessibility threshold filtering
- Cluster statistics view
BulkMulti
Integrated multi-omics analysis combining bulk RNA-seq with ATAC-seq data. Explore peak-to-gene linkages that connect regulatory elements to their target genes, view correlation scores between chromatin accessibility and gene expression across samples, and inspect the same signals in genomic context through the built-in landscape view.
- Peak-gene linkage visualization
- Correlation analysis
- Multi-omics data integration
- Landscape view with gene structure, tracks, and linkage arcs
Gene Info Outbound Links
Gene Browser provides direct links to external databases for additional information:
- JBrowse: View gene in genomic context with all available tracks
- Ensembl: Access detailed gene information from Ensembl database
- AnimalTFDB: Transcription factor family and binding site information
- InterPro: Protein domain and family classification
BLAST Search
SequenceServer
Find similar sequences in species-specific databases.
Key Features:
- Multiple BLAST programs
- Sequence alignment
- E-value filtering
- Results download
Available Databases:
- Genome sequences
- Ensembl cDNA
- Reference proteomes
Results Features:
- Detailed reports and diagrams
- FASTA sequences download
- JBrowse links for genome hits
- Shareable result IDs
Usage Tips:
- Choose appropriate BLAST program
- Adjust E-value threshold as needed
- Use genome database for context
- Save result IDs for sharing
Data Guide
Summary Statistics
The homepage and species pages use the following definitions for portal summary statistics.
Bulk runs
Number of public bulk omics sequencing runs currently included in the portal for this species. Each run usually corresponds to one SRA run accession, such as one SRR record. Multiple runs may be merged into one displayed sample group or genome-browser track.
Bulk bases
Total sequenced bases across the included public bulk runs, based on formal public-source audits plus any documented internal run-level bases evidence when applicable.
SC sample groups
Number of public single-cell sample groups currently included in the portal for this species. Each group corresponds to one public matrix displayed in Dash and can represent one or more source libraries or runs that were merged during curation.
Cells
Total cells across the included public single-cell sample groups, based on the metadata packaged with each published matrix.
Available Data Types
Genome and Gene Annotations
- Gene models and features
- Functional annotations
- GO and InterPro domains
BLAST Databases
- Genome sequences
- cDNA sequences
- Protein sequences
Bulk Omics Data
- Bulk RNA-seq
- Bulk ATAC-seq
- ChIP-seq
Single-cell Omics Data
- Single-cell RNA-seq
- Single-cell ATAC-seq
Major Updates
2020-10
First public release: Vue.js + R/Shiny, zebrafish and medaka.
2023-12
Expanded zebrafish data release.
2024-05
Four additional species added.
2026-07
Second-generation release: Hugo + Python/Dash, migration to a new server, public code release, turquoise killifish support, and expanded curated datasets.
Frequently Asked Questions
Resources
Project Resources
Contact and Collaboration
If you have questions about the portal or our datasets, please visit the Tu Lab homepage.
We also welcome collaborations with organism-specific communities interested in deploying miniODP on their own servers or hosting curated multi-omics datasets through our platform, and are happy to discuss potential collaborations.