seqMeta protocols

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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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Documentation


Maintainer


  • person_outline Brian Davis <>

Additional information


https://github.com/DavisBrian/seqMeta

seqMeta in pipelines

 (2)
2017
PMCID: 5509141
PMID: 28704393
DOI: 10.1371/journal.pone.0180046

[…] nhlbi exome sequencing project). variants were annotated using annovar [] and dbnsfp v2.0 according to grch37 and refseq. this multiple study snpinfo file was used as a component of the r package seqmeta (http://cran.rproject.org/web/packages/seqmeta/index.html)., we included age, sex, and apolipoprotein-e (apoe) as covariates in this investigation. apoe genotypes were determined using taqman […]

2016
PMCID: 5123402
PMID: 27884205
DOI: 10.1186/s13059-016-1106-x

[…] the range of the raw cadd scores and were introduced into the t5 burden test using its quartic form. the analytical models were the same as described above. all analyses were carried out using the r seqmeta package []., the significance threshold for the gene-based analysis is defined as p dis < 4.6 × 10−8 for the discovery stage adjusting for 15,589 genes and 70 amino acids and p rep < 0.0 […]


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seqMeta in publications

 (19)
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 […]

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 […]

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 […]

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 […]

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. […]


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