Qlucore Omics Explorer
Description
Qlucore Omics Explorer (Qlucore) is a graphical user interface (GUI) based package used for 'omics data anlaysis. Note that Qlucore Omics Explorer can analyze many types of 'omics data that are in tabular format (e.g., RNA seq count table, protein expression table, etc.).
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
- Pathway analysis
- Gene set enrichment
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 read mapping of NGS data, so users will have to rely on tools such as Partek Flow, Qiagen CLC Genomics Workbench, or Geneious Prime.
Things to Know
Despite having to run on a user's local machine, Qlucore Omics Explorer is able to complete many tasks such as differential expression analysis quickly.
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.