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Data import

Qlucore Omics Explorer supports a wide variety of data and file formats, see below. The Import Wizard provides great flexibility.

The program supports multi-omics analysis of 

  • mRNA (RNA-seg including single cell)
  • miRNA data
  • proteomics (assays, mass spec, Olink,…)
  • metabolomics
  • DNA Methylated data
  • qPCR
  • Flow cytometry
  • and more

The base module supports the following file formats:

  • Aligned BAM files (RNA-seq)
  • Olink (*.csv or *.parquet). Both vector and matrix structure
  • qPCR (normalized (delta-CT) or unnormalized (CT))
  • 10X Genomics Cell Ranger output files (MEX & H5)
  • Arbitrary count data using the import Wizard (*.txt, *.tsv, *.csv)
  • Arbitrary continuous data using the import Wizard (*.txt, *.tsv, *.csv)
  • ThermoFisher (Affymetrix) CEL files
  • Affymetrix Probe Set Files (*.chp)
  • Agilent text files (*.txt)
  • Agilent Gene View files (*.txt)
  • Qlucore Data files (*.gedata)
  • Simple Data files (*.txt)
  • Geo Data Sets (*.soft and *.soft.gz)
  • Geo Series Matrix (*.txt and *.txt.gz)
  • R data frame

The following files are supported for the NGS module:

  • bam files
  • vcf files
  • bed files
  • gtf files
  • txt files for gene fusions

Annotations

It is possible to import annotations (clinical or other information). The annotations should be stored in a .txt, .tsv, csv or .chip file. The Annotation Import Wizard makes it straightforward to import data from files with many different layouts.

R users

For users who also use R it is possible to export data to an R data frame and an R data frame can also be read.

Read about all features in Qlucore Omics Explorer.