visPIG protocols

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visPIG specifications

Information


Unique identifier OMICS_18992
Name visPIG
Alternative name VISual Plotting Interface for Genetics
Interface Web user interface
Restrictions to use None
Programming languages R
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Marc Henrion <>

Information


Unique identifier OMICS_18992
Name visPIG
Alternative name VISual Plotting Interface for Genetics
Software type Application/Script
Interface Command line interface, Graphical user 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
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Marc Henrion <>

Publication for VISual Plotting Interface for Genetics

visPIG in pipelines

 (2)
2018
PMCID: 5890276
PMID: 29632299
DOI: 10.1038/s41467-018-03178-z

[…] blocks were defined on the basis of hapmap recombination rate, as defined by using the oxford recombination hotspots, and on the basis of distribution of cis,. association plots were generated using vispig., classical hla alleles were imputed, both common and rare (a, b, c, dqa1, dqb1, drb1) and coding variants across the hla region using snp2hla. the imputation was based on a reference panel […]

2017
PMCID: 5711884
PMID: 29196614
DOI: 10.1038/s41467-017-00320-1

[…] (part of eigensoft) by merging cases and controls with phase iii hapmap samples. ld metrics were calculated in vcftools v0.1.12b, using uk10k merged 1000 genomes project data and plotted using vispig., the eight snps in the most promising loci (table ; supplementary table  ), were taken forward for de novo replication in an additional 1,284 cases from the nshlg and 2,504 controls […]


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visPIG in publications

 (12)
PMCID: 5890276
PMID: 29632299
DOI: 10.1038/s41467-018-03178-z

[…] blocks were defined on the basis of hapmap recombination rate, as defined by using the oxford recombination hotspots, and on the basis of distribution of cis,. association plots were generated using vispig., classical hla alleles were imputed, both common and rare (a, b, c, dqa1, dqb1, drb1) and coding variants across the hla region using snp2hla. the imputation was based on a reference panel […]

PMCID: 5849160
PMID: 29560096
DOI: 10.18632/oncotarget.23117

[…] []. cochran's q-statistic to test for heterogeneity and the i2 statistic to quantify the proportion of the total variation due to heterogeneity was calculated []. regional plots were generated using vispig software []. power calculations were performed using the methods described by skol et al. 2006 [], implemented via the web interface […]

PMCID: 5638070
PMID: 28771695
DOI: 10.1002/1873-3468.12778

[…] distances they span, which is unaddressed by most track browsers, can be addressed by sectioning tracks to display side‐by‐side only the ranges around two nodes being connected, as in washu and vispig . another approach is that of annular graphs, such as the archetypal circos browser, which tackle this with circular track showing transgenomic connections across the central area . […]

PMCID: 5253627
PMID: 28112199
DOI: 10.1038/srep41071

[…] defined as p < 5 × 10−8., ld between snps were calculated with vcftools using data from the uk10k (april 2014 release) and the 1000 genomes project (phase 1 v3). these data were plotted using vispig., to explore the epigenetic profile of genomic location associated with bcm, we used encode histone modification data and haploreg and regulomedb to examine whether any of the snps […]

PMCID: 4999417
PMID: 27524613
DOI: 10.1016/j.celrep.2016.07.053

[…] and non-blind fragments. profiles for the two classes of fragments were obtained at 100-bp resolution and an average profile for a 5-kb running window was computed. for data visualization, we used vispig () and incorporated processed chip-seq data from the encode project ()., allele-specific fragments of a 591-bp region spanning rs539846 were amplified from human genomic dna using primers […]


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visPIG institution(s)
Division of Genetics and Epidemiology, The Institute of Cancer Research, Surrey, UK; Department of Mathematics, Imperial College London, London, UK
visPIG funding source(s)
Supported by grants from the European Union (FP7/207-2013) under grant 258236, FP7 collaborative project SYSCOL and COST Action BM1206, Cancer Research UK (C1298/A8362-Bobby Moore Fund) and Leukaemia Lymphoma Research (LRF05001 and LRF06002); by an Erwin Schrodinger Fellowship from the Austrian Science Fund (FWF); by an Institute of Cancer Research (ICR)/Engineering and Physical Sciences Research Council (EPSRC) summer student bursary.

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