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Protocols

VSE specifications

Information


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
Requirements
parallel, IRanges, GenomicRanges, ggplot2, rmarkdown, knitr, igraph, car
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Hansen He

Publication for Variant Set Enrichment

VSE citations

 (34)
library_books

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

2018
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 […]

call_split

Bayesian nonparametric discovery of isoforms and individual specific quantification

2018
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 […]

library_books

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

2018
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 […]

library_books

Post earthquake health service support, Nepal

2018
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 […]

library_books

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

2018
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 […]

library_books

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

2018
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 […]

Citations

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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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