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seqMeta specifications

Information


Unique identifier OMICS_10386
Name seqMeta
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 2.0
Computer skills Advanced
Version 1.6.7
Stability Stable
Requirements
methods, Matrix, testthat, survival, R(≥3.1.0), SKAT, kinship2, coxme(≥2.2-4), CompQuadForm
Maintained Yes

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Maintainer


  • person_outline Brian Davis <>

Additional information


https://github.com/DavisBrian/seqMeta

seqMeta citations

 (20)
library_books

A Genome Wide Linkage Study for Chronic Obstructive Pulmonary Disease in a Dutch Genetic Isolate Identifies Novel Rare Candidate Variants

2018
PMCID: 5916965
PMID: 29725345
DOI: 10.3389/fgene.2018.00133

[…] rs cohorts (rs-i, rs-ii, and rs-iii), using the hrc imputed data (n = 11,372), the lls (n = 11,177), the vlavla cohort (n = 1,394) and the results (n = 11,797). for this analysis, in erf we used “seqmeta” package in r () to perform single-variant analysis, adjusted for age, sex, and smoking status (current/past/never smoking). logistic regression analysis was used to associate the variants […]

library_books

Whole exome sequencing identifies common and rare variant metabolic QTLs in a Middle Eastern population

2018
PMCID: 5780481
PMID: 29362361
DOI: 10.1038/s41467-017-01972-9

[…] data, with maf ≤ 5%, phwe > 10−6, and genotype call rate ≥90%. single-variant analysis was done using genabel package in r (as mentioned above for common variants), and burden test was done using seqmeta package in r (as in refs. ,). for burden tests, we accounted for the number of genes (n = 9823 genes; bonferroni p ≤ 6.16 × 10−9), and for single-variant analysis, we accounted for the number […]

library_books

Exome Wide Meta Analysis Identifies Rare 3′ UTR Variant in ERCC1/CD3EAP Associated with Symptoms of Sleep Apnea

2017
PMCID: 5651235
PMID: 29093733
DOI: 10.3389/fgene.2017.00151

[…] (ibm corp. released 2012. ibm spss statistics for windows, version 21.0. armonk, ny: ibm corp.). study specific exome analyses and meta-analysis of the individual study data were performed using the seqmeta v1.5 library of the r software (http://cran.r-project.org/web/packages/seqmeta/). single variant association analysis was performed by assuming an additive effect. in erf and fhs a linear […]

library_books

Rare coding variants pinpoint genes that control human hematological traits

2017
PMCID: 5560754
PMID: 28787443
DOI: 10.1371/journal.pgen.1006925

[…] while fibrinogen levels were assessed using the clauss method []. association analyses in the fhs were conducted using either raremetalworker (http://genome.sph.umich.edu/wiki/raremetalworker) or seqmeta (http://cran.r-project.org/web/packages/seqmeta/index.html). a linear mixed effects model that accounts for familial correlation was used and adjustments were made for age, sex and principal […]

library_books

Mutation intolerant genes and targets of FMRP are enriched for nonsynonymous alleles in schizophrenia

2017
PMCID: 5669020
PMID: 28719003
DOI: 10.1002/ajmg.b.32560

[…] variants) in a gene. this maf threshold was chosen because it captured the greatest proportion of the rare variant signal in a exome‐sequencing study of schizophrenia (fromer et al., ). we used seqmeta 1.6.5 (urls) available in r for meta‐analysis of the united kingdom and swedish cohorts to calculate unified sequencing kernel association (skat‐o) tests and burden tests for genes. […]

library_books

Whole exome sequence based association analyses of plasma amyloid β in African and European Americans; the Atherosclerosis Risk in Communities Neurocognitive Study

2017
PMCID: 5509141
PMID: 28704393
DOI: 10.1371/journal.pone.0180046

[…] were linearly regressed onto age, gender, apoe ε4 carrier status, and time elapsed between visits (fold-changes only) separately by race. following inverse normal transformation of the residuals, seqmeta was used to conduct race-specific single-variant and gene-based association tests while adjusting for population structure. linear regression models were fit on autosomal variants with minor […]


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