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BioTool

Omics data & analysis

31 resources · Explore transcriptomics, single cells, epigenomics, proteomics, metabolomics and microbiomes.

GEO

Find gene expression and functional genomics datasets.
Transcriptomics
Database

Expression Atlas

Explore gene expression across tissues, conditions and species.
Transcriptomics
Database

GTEx

Explore human tissue gene expression and genetic regulation.
Transcriptomics
Database

CELLxGENE

Find, explore and download single-cell datasets.
Single-cell data
Database / online tool

UCSC Cell Browser

Visualize single-cell datasets and gene expression.
Single-cell data
Data browser

Single Cell Portal

Find and visualize single-cell research data.
Single-cell data
Data platform

Seurat

Integrate, cluster and analyze single-cell data.
Single-cell & spatial analysis
R package

Scanpy

Preprocess, cluster and analyze single-cell data.
Single-cell & spatial analysis
Python package

Squidpy

Analyze spatial single-cell data and images.
Single-cell & spatial analysis
Python package

ENCODE

Find genomic functional elements and epigenetic regulation data.
Epigenetics & regulation
Database

JASPAR

Look up transcription factor binding motifs.
Epigenetics & regulation
Database

Cistrome

Find and analyze chromatin and transcriptional regulation data.
Epigenetics & regulation
Database / toolkit

PRIDE

Find mass spectrometry proteomics data.
Proteomics
Database

ProteomeXchange

Find proteomics datasets across participating resources.
Proteomics
Data portal

Skyline

Analyze quantitative mass spectrometry data.
Proteomics
Desktop software

MetaboAnalyst

Perform metabolomics statistics, enrichment and pathway analysis.
Metabolomics
Online tool

HMDB

Look up human metabolites, spectra and related information.
Metabolomics
Database

Metabolomics Workbench

Find metabolomics datasets and analysis resources.
Metabolomics
Database / toolkit

MGnify

Explore microbiome data and analysis results.
Microbiomes
Data analysis platform

MicrobiomeAnalyst

Perform statistical, functional and visualization analyses of microbiomes.
Microbiomes
Online tool

SILVA

Find ribosomal RNA reference sequences and taxonomy.
Microbiomes
Database

ArrayExpress (BioStudies)

Find functional genomics experiments and accompanying data in BioStudies.
Expression datasets
Database

GSA-Human

Find human genetic and omics datasets with public or controlled access.
Human omics data
Database

Human Cell Atlas Data Portal

Access datasets from human cell atlas research.
Human cell atlases
Data portal

HuBMAP Data Portal

Explore human tissue, cell and spatial multi-omics data.
Spatial & tissue atlases
Data portal

iProX

Submit, find and share proteomics datasets.
Proteomics data
Database

MetaboLights

Find metabolomics experiments and their metadata.
Metabolomics data
Database

LIPID MAPS

Find lipid structures, classifications, nomenclature and related data.
Lipidomics
Database / tools

QIIME 2

Process and analyze microbiome data with traceable analysis provenance.
Microbiome analysis
Analysis software

DESeq2

Analyze differential expression from sequencing count data.
Differential expression
Software package

FastQC

Generate quality-control reports for sequencing reads.
Sequencing quality control
Desktop software / command line