Software Packages

Department of Quantitative Health Sciences
Mayo Clinic Research
Formerly known as the Department of Health Sciences Research

Related links: Division Overview R Shiny Applications


ICQ-lincRNA (Identification, Characterization, and Quantification of Long Intergenic Non-Coding RNAs), offers an end-to-end solution to identify and annotate expressed lincRNAs in next generation RNA sequencing data.  Specifically, ICQ-lincRNA:

  • Conducts ab-initio genome-wide transcript assembly by both Cufflinks and Scripture using Binary Alignment/Map (BAM) files
  • Conducts downstream quantitative analyses including gene count, exon count, overlap with known lincRNAs annotated by GENCODE V12 and Broad lincRNA Catalog (
  • Annotates lincRNAs with neighboring protein-coding genes, and chromatin map status in nine human cell lines from ENCODE project
  • Provides a comprehensive HTML report for all samples analyzed

ICQ-lincRNA provides three modes of execution:

1)      A Virtual Machine (VM) mode (to demonstrate the workflow only)

2)      Standalone single machine mode

3)      Parallel Sun Grid Engine cluster mode

Downloads are available for:

Please contact if you have additional questions.

Page last modified: January 7, 2018