Omics Playground: Explore Omics Data Freely

Omics Playground is a comprehensive self-service platform platform for visualization, analytics and exploration of Big Omics Data. It allows users to apply a multitude of state-of-the-art analysis tools to their own data to explore and discover underlying biology in a short time.

The platform offers a unique combination of features that distinguishes it from the other analytics platforms currently available. We believe that data preprocessing (primary analysis) and statistical testing (secondary analysis) are now well established, and the most challenging task is currently data interpretation (tertiary analysis) that often takes the longest time but where actual insights can be gained. Therefore Omics Playground focuses strongly on tertiary analysis while providing good support for secondary analysis.

Getting Started

• Overview

Basic Data Preparation

• Introduction
  • Input file requirements
• Samples file
• Counts file
• Contrasts file (optional)
  • Sample-wise contrast (long form)
  • Group-wise contrasts (short form)
• Checks before uploading
• Uploading your data in Omics Playground

Advanced Data Preparation

• What if I have many datasets?
• Preparing input files from raw data formats
  • From FASTQ files
  • From gene counts table or GEO repository
  • From single-cell data
  • From LC-MS/MS proteomics data
• Loading custom geneset files
• Data processing inside Omics Playground
  • Filtering of features (genes) and samples
  • Normalisation
  • Offline computation

Analysis Modules

• Outline
  • Main menu
  • Help menu
  • User menu
  • Figure & table tags
  • Glossary
• Load Panel
  • Selecting a dataset
  • Load (Upload new)
  • Upload new (Comparisons)
  • Upload new (Compute)
• Data View
  • Settings panel
  • Gene Overview
  • Sample QC
  • Counts Table
  • Sample Information
  • Contrasts
• Clustering
  • Samples
    • Settings panel
    • Heatmap
    • Annotate clusters
    • PCA/tSNE
    • Parallel
  • Features
    • Settings panel
    • Gene and Geneset UMAP settings
    • Gene
    • Geneset
• Expression
  • Differential expression
    • Settings panel
    • Table
    • Foldchange (all)
    • FDR table
    • Overview Plots
    • Top genes
    • Volcano by comparison
    • Volcano by method
  • Correlation analysis
    • Settings panel
    • Correllation
    • Graph
  • Find Biomarkers
    • Settings panel
    • Feature Selection
    • Feature-set Ranking
• GeneSets
  • Geneset enrichment
    • Settings panel
    • Top enriched gene sets
    • Frequency in top gene sets
    • Table
    • Genes in gene set
    • Geneset expression
    • Enrichment by comparison
    • Volcano by comparison
    • Volcano by method
    • Enrichment (all)
    • FDR table
  • Test geneset
    • Settings panel
    • Enrichment table
    • Volcano plots
    • Enrichment
    • Overlap/similarity
    • Markers
  • Pathway analysis
    • Settings panel
    • WikiPathways
    • Reactome
    • GO graph
  • Word Cloud
    • Settings panel
    • Main panel
• Compare
  • Compare signatures
    • Settings panel
    • Pairwise scatter
    • Signature clustering
  • Compare datasets
    • Settings panel
    • Compare expression
    • Fold change
    • Gene correlation
  • Similar experiments
    • Settings panel
    • FC correlation
    • FC heatmap
    • Meta-network
• SystemsBio
  • Drug connectivity
    • Settings panel
    • Drug enrichment
  • Cell Profiling
    • Settings panel
    • Cell type
    • Mapping
    • Markers
  • WGCNA
    • Settings panel
    • WGCNA
    • Modules
    • Eigengenes
    • Intramodular

Examples

• Reanalyzing Public Datasets
  • Single-cell RNA-seq data
  • Bulk RNA-seq Data
  • Microarray Data
  • Proteomic Data

Methods

• Methods
  • Batch correction
  • Clustering
  • Statistical testing
  • Functional analysis
  • Cell type profiling
  • Scripting and visualization
  • REFERENCES

FAQ

• Frequently Asked Questions (FAQ)
  • Can I use LIMMA, EdgeR and DESeq2 for my proteomics data?
  • How are duplicated gene/protein names handled in the counts file?
  • How are “missing values” handled in the counts file?
  • How do I switch between stable, beta & testing docker versions?

About

• Contact
• Citation
• License