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VSE specifications


Unique identifier OMICS_16331
Name VSE
Alternative name Variant Set Enrichment
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.99
Stability Stable
parallel, IRanges, GenomicRanges, ggplot2, rmarkdown, knitr, igraph, car
Maintained Yes


No version available



  • person_outline Hansen He

Publication for Variant Set Enrichment

VSE citations


A catalog of potential putative functional variants in psoriasis genome wide association regions

PLoS One
PMCID: 5929547
PMID: 29715312
DOI: 10.1371/journal.pone.0196635

[…] To evaluate and characterize the pattern of psoriasis tagSNPs in functional genomics data of psoriasis relevant cells, we implemented an enrichment test through variant set enrichment (VSE) R package []. We identified 26 types of human primary cells/cell lines, mainly primary immune cells and skin keratinocytes cells, in NIH Roadmap Epigenomics Consortium. They have been widely sugg […]


Bayesian nonparametric discovery of isoforms and individual specific quantification

Nat Commun
PMCID: 5923247
PMID: 29703885
DOI: 10.1038/s41467-018-03402-w
call_split See protocol

[…] nscripts of SNCA might be interesting targets for future research and demonstrate the unique utility of biisq.To further characterize the functional relationships among these cis-trQTLs, we performed variant set enrichment (VSE) analysis for regions associated with variable intron splicing events identified by LeafCutter, which identifies regions that associate spatially with splicing QTLs and cis […]


Genome wide association study identifies susceptibility loci for B cell childhood acute lymphoblastic leukemia

Nat Commun
PMCID: 5890276
PMID: 29632299
DOI: 10.1038/s41467-018-03178-z

[…] To assess for an over-representation of markers for open chromatin the variant set enrichment method of Cowper-Sal Lari et al. was adapted. For each risk locus, SNPs in LD were defined (i.e., R2 > 0.8 and D′ > 0.8), and termed associated variant set (AVS). Transcription […]


Post earthquake health service support, Nepal

Bull World Health Organ
PMCID: 5872014
PMID: 29695885
DOI: 10.2471/BLT.17.205666

[…] В декабре 2015 года наиболее пострадавшие от землетрясения люди все еще жили во временных убежищах, предоставление медицинских услуг было ограниченно, только пять из 14 пострадавших от землетрясения районов предоставляли отчетность о заболеваниях в Министерство зд […]


Untreated depression and tuberculosis treatment outcomes, quality of life and disability, Ethiopia

Bull World Health Organ
PMCID: 5872008
PMID: 29695881
DOI: 10.2471/BLT.17.192658

[…] В исследовании участвовали 648 взрослых пациентов с туберкулезом, последовательно поступивших в 14 учреждений первичной медико-санитарной помощи. Все они прошли оценку в начале лечения (т. е. на исходном уровне), затем через 2 и 6 месяцев. Авторы считали депрессию вероятной, если пациент набирал 10 баллов и выше по шкале опросника о здоровье па […]


Re analysis of public genetic data reveals a rare X chromosomal variant associated with type 2 diabetes

Nat Commun
PMCID: 5778074
PMID: 29358691
DOI: 10.1038/s41467-017-02380-9

[…] t enrichment analysis, p = 3.9 × 10−8, FDR = 0.05, Supplementary Data , Supplementary Fig. , Supplementary Fig. ), in concordance with the current knowledge of the molecular basis of T2D.In addition, variant set enrichment analysis of the T2D-associated credible sets across regulatory elements defined in isolated human pancreatic islets showed a significant enrichment for active regulatory enhance […]


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VSE funding source(s)
This work was supported by PMCF, CFI and ORF (CFI32372), NSERC (498706), WICC and CCS (703800), CCSRI (702922), PCC (RS2016-02 and RS2014-04), CIHR (142246), NCI at the NIH (R01CA155004, LM009012 and LM010098).

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