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MetaGen specifications

Information


Unique identifier OMICS_22084
Name MetaGen
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, R, Shell (Bash)
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 1.1.0
Stability Stable
Requirements
Ray Assembler or MegaHIT Assembler, Bowtie2, Samtools, Repp, MASS, mixtools, doParallel, foreach, seqinr, getopt
Maintained Yes

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Maintainer


  • person_outline Wenxuan Zhong <>

Publication for MetaGen

MetaGen in publications

 (19)
PMCID: 5943621
PMID: 29774017
DOI: 10.3389/fmicb.2018.00872

[…] community studies., besides genes or species, assembled contigs have also been used as features to predict disease. several contig binning tools, such as concoct (), maxbin2.0 (), cocacola (), and metagen (), were developed for binning contigs assuming that contigs with similar coverage/relative abundances over different samples come from the same genomes. in particular, although the main […]

PMCID: 5940131
PMID: 29708498
DOI: 10.18632/aging.101424

[…] 3723 genes not measured in 6 or more of the 18 independent experiments, yielding a final set of 12781 genes for inclusion in the random effects meta-analysis model (r package: meta, r function: metagen). for this approach, the dersimonian-laird estimate was used to calculate a meta-fc for each gene with inverse variance weighting (i.e., greater weight assigned to experiments associated […]

PMCID: 5617696
PMID: 28930829
DOI: 10.1097/MD.0000000000007946

[…] reviewer was performed to come to a consensus., meta-analysis was conducted using r 3.12 software (r foundation for statistical computing, beijing, china; http://www.r-project.org) with function metagen, metabin, metabias, etc. (r package: meta). the hazard rates (hrs) or odds ratios (ors), as well as their 95% confidence intervals (cis), were selected as the effect indexes for evaluating […]

PMCID: 5553996
PMID: 28153336
DOI: 10.1016/j.biopsych.2016.12.012

[…] the full dataset at the time of this study). meta-analysis was performed across all cohorts in each group to generate group-level association statistics. the meta-analysis was performed using the “metagen” function in the r package “meta”. for the ds sample the gwas summary statistics were downloaded from the website of the social science genetic association consortium […]

PMCID: 5559542
PMID: 28814741
DOI: 10.1038/s41598-017-08595-6

[…] the mixed-effects model was fitted using the lmer function from the r package lme4. the linear regression was fitted using the lm function in r. the meta-analysis was performed using the metagen function from the r package meta. the mcnemar’s test, t-test, binomial test were performed using the mcnemar. test, t. test and binom. test function in r, respectively., the discovery data […]


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MetaGen institution(s)
Department of Statistics, University of Georgia, Athens, GA, USA; Department of Statistics, Harvard University, Cambridge, MA, USA; Center for Statistical Science & Department of Industry Entering, Beijing, China
MetaGen funding source(s)
Supported in part by the National Institutes of Health (grant R01 GM113242-01); and the National Science Foundation (grants DMS-1440038 and DMS-1440037).

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