UNCeqR statistics

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Associated diseases

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UNCeqR specifications

Information


Unique identifier OMICS_19334
Name UNCeqR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Tumor DNA-WES or tumor RNA-seq.
Operating system Unix/Linux
Programming languages Perl, R
License MIT License
Computer skills Advanced
Version 0.2
Stability Stable
Requirements
grep, cat, sed, date, md5sum, VGAM, multicore, Getopt::Long, Math::CDF, Math::Cephes
Maintained Yes

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Maintainer


  • person_outline Matthew Wilkerson <>

Publication for UNCeqR

UNCeqR in pipeline

2015
PMCID: 4468211
PMID: 26076459
DOI: 10.1371/journal.pone.0129280

[…] by analysis of rna-seq data using two independent mutation calling algorithms: the samtools (mpileup command)/bcftools [] and our recently published rnaseq-specific mutation calling method, unceqr []., for the 07–0120 tumor tissue cohort, we have previously performed sanger sequencing using a dna analyzer (abi 3730xl, applied biosystems, foster city, ca) for mutation detection […]


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UNCeqR in publications

 (4)
PMCID: 5760704
PMID: 29317634
DOI: 10.1038/s41467-017-02428-w

[…] detected by other methods (fig. ). in one sample (a8kf), we detected a bap1 mutation that was initially filtered out due to low exome coverage but was “rescued” with matched rna-seq data using unceqr (fig. ). in addition, due to the design of baits for exome capture, large deletions that start or end in intronic or promoter regions can be missed using wes data. in three samples (aa8p, […]

PMCID: 5666005
PMID: 29093439
DOI: 10.1038/s41467-017-01174-3

[…] (absolute copy) were plotted after adjustment for normal contamination., somatic snvs identified by freebayes from wgs data were validated by detecting the snvs in matched rna-seq data using unceqr, in “interrogate” mode. rna-seq data were aligned using rsubread as described in “rna-seq data processing.” each patient’s somatic snvs were input into unceqr in the form of a bed file […]

PMCID: 5477513
PMID: 28548104
DOI: 10.1038/ncomms15290

[…] and sequenced by illumina hiseq2000 with a total of 10 gb data. rna reads were aligned to the hg19 genome assembly using mapsplice. to confirm snvs reported in the wgs dna samples, we applied unceqr to call somatic variants from rna-seq data. gene expression using rsem was quantified for the transcript models corresponding to the tcga gaf2.1 and normalized to a fixed upper quartile […]

PMCID: 4468211
PMID: 26076459
DOI: 10.1371/journal.pone.0129280

[…] by analysis of rna-seq data using two independent mutation calling algorithms: the samtools (mpileup command)/bcftools [] and our recently published rnaseq-specific mutation calling method, unceqr []., for the 07–0120 tumor tissue cohort, we have previously performed sanger sequencing using a dna analyzer (abi 3730xl, applied biosystems, foster city, ca) for mutation detection […]


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UNCeqR institution(s)
Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; The Genome Institute at Washington University, St. Louis, MO, USA; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Internal Medicine, Division of Medical Oncology, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
UNCeqR funding source(s)
Supported by National Cancer Institute [F32CA142039, Breast SPORE P50-CA058223]; National Institutes of Health [U24 CA143848 and U24 CA143848-02S1].

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