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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.