Omics Playground Tutorials
Dasboard Overview, Data Preparation and Upload guidelines
1. ABCs of Omics Playground: Understanding the Dashboard Layout
2. How to Prepare your Data for the Upload
How to Convert FASTQ files into read count tables using Galaxy
If you have FASTQ files, you’ll need to convert them into read counts before uploading them to the platform. Follow this guide to perform the conversion using Galaxy.
3. How to Upload your Data to Omics Playground
Analysis modules
1. Clustering Analysis:
PCA/t-SNE, Heatmap, Gene and Geneset Clustering
This video guides you through the different clustering options available in Omics Playground. Key points covered:
Platform overview and resources
How to visualize data using dimensionality reduction (e.g., UMAP, PCA, tSNE) for clustering analysis.
Look at dynamic or static heatmaps to visualize gene expression, customize by phenotypes, and explore gene families or custom gene lists.
Perform gene set or pathway-level analysis, highlighting hotspots of variation across samples and correlating them with disease outcomes.
2. Expression Analysis:
Differential Gene or Protein Expression, Correlation and Biomarkers
Learn more about the expression analysis module in Omics Playround. Here you can:
Perform differential gene or protein expression analysis using volcano and MA plots.
Compare gene expression across pairwise comparisons and compare results from different statistical methods.
Use correlation analysis to identify genes with similar expression patterns to a selected target gene.
Identify potential biomarkers based on gene expression differences, with customization options to focus on specific gene families or custom gene lists.
3. GeneSets Module:
Gene or Protein Set Enrichment Analysis and Pathway Analysis
Learn more about enrichment and pathway analysis options in Omics Playground. This video covers:
- Visualizing gene set enrichment with GSEA plots
- Testing your own gene sets and viewing their expression across comparisons.
- Performing pathway analysis using WikiPathways and Reactome collections.
- Generating and customizing word clouds for data presentation.
4. Compare Module:
Compare Signatures, Similar Experiments and Datasets
Learn more about comparative analysis options in Omics Playground. This video covers:
- Producing scatter plots and Venn diagrams for pairwise comparisons within your dataset.
- Extending comparative analysis across different datasets.
- Comparing specific pairwise comparisons within your dataset to others you’ve uploaded.
- Accessing a database of over 6,000 experiments from the GEO database for broader comparisons.
5. SystemsBio and DataView Modules: WGCNA, Cell Profiling, Drug Connectivity and Data View
This video covers the analysis options available in the SystemsBio and DataView modules in Omics Playground. The video particularly focuses on how you can:
- Identify the mode of action of a drug that you’re testing.
- Identify drugs that could be repurposed to treat a condition.
- Identify potential genes that could be targeted for intervention through the gene perturbation map.
- Using the sensitivity collection, identify potential partner drugs with synergistic effects to the drugs you’re currently testing.
- Use the DataView module to have a more detailed look at target genes or proteins.
