Qlucore Omics Explorer
Description
Qlucore Omics Explorer (Qlucore) is a graphical user interface (GUI) based package used to generate visualizations, elucidate biological function, and classify samples as well as cells for omics data.
Listing of Analysis Functions
Omics analyses
- Gene expression data derived from
- Microarray
- RNA or single cell RNA sequencing
- qPCR
- miRNA derived from microarray or sequencing
- Proteomics
- Metabolomics
- Lipidomics
Flow cytometry
Epigenetics
- Methylation (microarray)
Biological insights
- Gene set enrichment
- Gene ontology
Machine learning based sample and cell classifcation
- K nearest neighbor
- Support Vector Machines
- Random Trees
- Gradient boosted trees
Identify biomarkers
Visualizations
- PCA plots
- t-SNE plots
- Heat maps with hierarchical clustering
- Scatter plots
- Volcano plots
- Box plots
Interactive statistical analysis tools
- Two group comparison (t-test)
- Paired t-test
- Multi-group comparison (F-test) (ANOVA)
- Two-way ANOVA
- Linear, quadratic, and rank regression
Recommendations
Qlucore Omics Explorer does not perform upstream tasks in Next Generation Sequencing such as quality control, read mapping, or deriving gene expression counts. Use Partek Flow, Qiagen CLC Genomics Workbench, or Geneious Prime.
Things to Know
Qlucore Omics Explorer specializes in taking tabular omics data (e.g, RNA sequencing read counts) and producing robust visualizations. If an investigator is interested only in visualizations rather than tabular outputs, this would be the goto package.
Input Data Types
Standard formats generally accepted:
- BAM
- GTF
- QUANT.sf (Qlucore)
- GEDATA (Qlucore)
- CEL
- CHP
- BioArray Software Environment
- TXT
- CSV
- GEO
- SRA
- CYTOBAND
- 10X GENOMICS (requires barcodes.tsv, features.tsv, matrix.mtx)
Output Data Types
Images
- PNG
- JPG
- BMP
- TIF
Tabular data
- GEDATA (Qlucore)
Access Information
You must submit a request through service.cancer.gov to obtain access to Qlucore Omics Explorer. This software requires access to a floating license server (OSTR has 5 licenses). Please be sure to close the application when you are finished so the license becomes available to others. To use Qlucore Omics Explorer, a connection to the NIH network or VPN is necessary.
Getting help
Qlucore Omics Explorer has extensive documentation. To access these, users will need to create an account on the Qlucore Omics website. There are also webinars that showcase the use of various workflows. BTEP also hosts Qlucore Omics training on a frequent basis, check the Video Archive for recordings of previous classes. Look out for future training on the BTEP calendar.