metagenomeSeq protocols

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metagenomeSeq specifications

Information


Unique identifier OMICS_07813
Name metagenomeSeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.22.0
Stability Stable
Requirements
limma, methods, RColorBrewer, gplots, parallel, BiocGenerics, Biobase, Matrix, knitr, R(>=3.0), foreach, matrixStats, annotate, gss, vegan, glmnet, biomformat, testthat(>=0.8), interactiveDisplay
Maintained Yes

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Maintainer


  • person_outline Joseph N. Paulson <>

Publication for metagenomeSeq

metagenomeSeq in pipelines

 (10)
2017
PMCID: 5335496
PMID: 28253908
DOI: 10.1186/s40168-017-0237-y

[…] statistical tests needs to be investigated., thanks to mcmurdie and holmes’ previous work in this area [], we recognize the potential of these newer techniques and have incorporated deseq2 [] and metagenomeseq [, ] normalization and differential abundance testing into qiime version 1.9.0 [], along with the traditional rarefying and non-parametric testing techniques. ancom differential […]

2017
PMCID: 5374497
PMID: 28361981
DOI: 10.1038/srep45651

[…] 3000 reads were removed from the analysis. thus, 261 subjects were included in downstream analyses. due to large variation in library sizes, the read counts were normalized using the css method from metagenomeseq package v.1.11 in r v. 3.2.4. all 16s rrna gene sequences have been deposited in the european nucleotide archive (accession no. prjeb14627; […]

2017
PMCID: 5507859
PMID: 28701764
DOI: 10.1038/s41598-017-05662-w

[…] with a low sequencing depth (<500 reads) were discarded. a rarefaction plot can be found in supplementary material (supplementary figure ). otu tables were normalized with the abundance-based metagenomeseq’s cumulative sum scaling (css) transformation using the qiime script normalize_table.py. the normalized otu table was used for all downstream analysis., for all downstream analysis, […]

2017
PMCID: 5596945
PMID: 28899340
DOI: 10.1186/s12864-017-4111-x

[…] to the same genome annotation downloaded from http://www.gencodegenes.org/releases/19.html., we performed principal component analysis (pca) as implemented in the plotord function on the r package metagenomeseq 1.12.1. pca was applied to the full expression data matrix., differential expression analysis was performed using voom available in the limma bioconductor r package (version 3.26.9) []. […]

2017
PMCID: 5708741
PMID: 29190829
DOI: 10.1371/journal.pone.0188873

[…] ] using the greengenes taxonomy (greengenes99 database version 12.10) []. additional details are provided in ., to account for dispersion and sparsity, microbial reads were normalized with the metagenomeseq package []. we used the bray-curtis dissimilarity measure, a count-based measure to compare between two sampling sites, traditionally employed in ecological studies [–]. to identify […]


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metagenomeSeq in publications

 (78)
PMCID: 5943489
PMID: 29774014
DOI: 10.3389/fmicb.2018.00862

[…] index, simpson index, and shannon index) and β-diversity (bray curtis dissimilarity) measurements were calculated based on the normalized data of the cumulative sum scaling (css) transformation of metagenomeseq (paulson et al., ). canonical correspondence analysis (cca) and constrained principal coordinate analysis (cpcoa) were used to visualize the data. the differential abundances of otus […]

PMCID: 5928236
PMID: 29740420
DOI: 10.3389/fmicb.2018.00792

[…] (otus) with the silva 16s database () in qiime (). all sequences taxonomically assigned to chloroplasts were removed from further downstream analysis. when appropriate, data was normalized using metagenomeseq’s cumulative sum scaling to account for uneven sampling depth ()., to visualize the relative abundance of bacterial phyla, stacked bar charts were generated using ggplot2 (). […]

PMCID: 5923500
PMID: 29677122
DOI: 10.3390/v10040206

[…] were detected in the oral microbiota composition of fiv-infected cats relative to naïve animals (a). normalized data were tested using the zero inflated gaussian model implemented in the r package metagenomeseq [] to identify the putative otus driving differences between fiv+ and fiv− cats. significant log-fold change in abundance in 12 genera was noted between groups at the 0.1 level […]

PMCID: 5910605
PMID: 29678163
DOI: 10.1186/s12864-018-4637-6

[…] \setlength{\oddsidemargin}{-69pt} \begin{document} $$ n_{j} = \sum_{i:y_{ij} \leq q_{j}^{\hat{l}}} y_{ij}. $$ \end{document}nj=∑i:yij≤qjl^yij. css normalization was done using metagenomeseq bioconductor package (version 1.10.0) []., reversed cumulative sum scaling (rcss) is a variant of css that utilize the observation that high-abundant genes in shotgun metagenomic data […]

PMCID: 5897366
PMID: 29651035
DOI: 10.1038/s41598-018-24280-8

[…] amr and kraken results were normalized at each sequencing depth using a data-driven approach based in shifts in the distributions of counts called cumulative sum scaling (css) normalization of the metagenomeseq package of r. normalized counts were then aggregated at each of the taxonomic levels (phylum, class, order, family, genus, and species) and the antimicrobial resistance classification […]


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metagenomeSeq institution(s)
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA

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