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MetaBin specifications

Information


Unique identifier OMICS_17892
Name MetaBin
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Advanced
Version 1.0
Stability Stable
Maintained No

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Maintainer


This tool is not available anymore.

Additional information


(Sharma et al., 2012) Fast and Accurate Taxonomic Assignments of Metagenomic Sequences Using MetaBin. PLoS One. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0034030

Information


Unique identifier OMICS_17892
Name MetaBin
Interface Web user interface
Restrictions to use None
Input data A metagenomic sequence.
Input format FASTA format
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained No

Maintainer


This tool is not available anymore.

Additional information


(Sharma et al., 2012) Fast and Accurate Taxonomic Assignments of Metagenomic Sequences Using MetaBin. PLoS One. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0034030

MetaBin in publications

 (8)
PMCID: 5617696
PMID: 28930829
DOI: 10.1097/MD.0000000000007946

[…] 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: 5601770
PMID: 28938674
DOI: 10.18632/oncotarget.19810

[…] 20,000-simulation burn-in phase. direct probability statements were derived from an additional 50,000-simulation phase []. thirdly, with the r 3.2.1 software, two-category data was produced by using metabin function. with or as effect size, mantel-haenszel method was used to calculate fixed effect model or random effect model. when p > 0.05, we chose fixed effect model otherwise we chose […]

PMCID: 5149528
PMID: 28018298
DOI: 10.3389/fmicb.2016.01952

[…] shown in figure ., analyses were performed in r version 3.3.1 (r development core team, ), using functions from packages “meta” (schwarzer, ) and “metaphor” (viechtbauer, ). we used the “metabin” function to transform the count data into the (log-) odds ratio described above. we then weighted these values by the inverse of their respective squared standard errors, and pooled […]

PMCID: 4828583
PMID: 27148174
DOI: 10.3389/fmicb.2016.00469

[…] a homology-based or a composition-based approach, or a combination of these two approaches (sharma et al., ). among the two approaches, the homology-based methods, such as megan (huson et al., ) and metabin (sharma et al., ), are more sensitive and accurate, but suffer primarily due to the time required to generate the blast or blat alignments. the composition-based or marker-gene based […]

PMCID: 4634789
PMID: 26537885
DOI: 10.1186/s12859-015-0788-5

[…] and precision were recalculated after reclassifying overpredictions as correct classifications (fig. ). there was notable increase in sensitivity and precision for methods such as megan4 and metabin which are less conservative in their predictions. for more conservative methods such as carma3 and discribinate, there was little change.fig. 3, the changes in sensitivity, precision, […]


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MetaBin institution(s)
Laboratory for MetaSystems Research, Quantitative Biology Center, RIKEN, Yokohama, Kanagawa, Japan, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India
MetaBin funding source(s)
This work was supported by the operational expenditure fund of RIKEN.

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