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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.