metagenomeSeq statistics

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Citations per year

Number of citations per year for the bioinformatics software tool metagenomeSeq
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Tool usage distribution map

This map represents all the scientific publications referring to metagenomeSeq per scientific context
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Associated diseases

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Popular tool citations

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Protocols

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

Versioning


No version available

Documentation


Maintainer


  • person_outline Joseph N. Paulson

Publication for metagenomeSeq

metagenomeSeq citations

 (76)
call_split

Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging

2018
Front Microbiol
PMCID: 5943489
PMID: 29774014
DOI: 10.3389/fmicb.2018.00862
call_split See protocol

[…] ao 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 bet […]

call_split

Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations

2018
Front Microbiol
PMCID: 5928236
PMID: 29740420
DOI: 10.3389/fmicb.2018.00792
call_split See protocol

[…] nits (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 (). In addition, […]

library_books

Applications of the FIV Model to Study HIV Pathogenesis

2018
Viruses
PMCID: 5923500
PMID: 29677122
DOI: 10.3390/v10040206

[…] es 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 of signif […]

call_split

Comparison of normalization methods for the analysis of metagenomic gene abundance data

2018
BMC Genomics
PMCID: 5910605
PMID: 29678163
DOI: 10.1186/s12864-018-4637-6
call_split See protocol

[…] least the 50th percentile. The normalization factor for sample j is then computed as the sum over the genes counts up to the threshold qjl^, i.e. 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 have […]

call_split

Impact of sequencing depth on the characterization of the microbiome and resistome

2018
Sci Rep
PMCID: 5897366
PMID: 29651035
DOI: 10.1038/s41598-018-24280-8
call_split See protocol

[…] s, 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 le […]

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Fungal community profiles in agricultural soils of a long term field trial under different tillage, fertilization and crop rotation conditions analyzed by high throughput ITS amplicon sequencing

2018
PLoS One
PMCID: 5886558
PMID: 29621291
DOI: 10.1371/journal.pone.0195345
call_split See protocol

[…] , Cluster 3.0 was used []. PCA was conducted to further describe the similarity between the fungal communities of different samples. Differentially abundant OTUs were identified by application of the metagenomeSeq Bioconductor package (v1.1.16), []. The approach implements a novel normalization technique and a statistical model addressing under-sampling in high-throughput sequencing projects. The […]


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

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