Normalization and microbial differential abundance strategies depend upon data characteristics
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Title
Normalization and microbial differential abundance strategies depend upon data characteristics
Authors
Keywords
Microbiome, Normalization, Differential abundance, Statistics
Journal
Microbiome
Volume 5, Issue 1, Pages -
Publisher
Springer Nature
Online
2017-03-03
DOI
10.1186/s40168-017-0237-y
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Note: Only part of the references are listed.- zCompositions — R package for multivariate imputation of left-censored data under a compositional approach
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- (2014) Joseph N Paulson et al. NATURE METHODS
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- (2014) Mihai Pop et al. GENOME BIOLOGY
- voom: precision weights unlock linear model analysis tools for RNA-seq read counts
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- (2014) Andrew D Fernandes et al. Microbiome
- Variable selection for sparse Dirichlet-multinomial regression with an application to microbiome data analysis
- (2013) Jun Chen et al. Annals of Applied Statistics
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- (2013) Danni Yu et al. BIOINFORMATICS
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- (2013) Charlotte Soneson et al. BMC BIOINFORMATICS
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- (2013) Catherine A. Lozupone et al. Cell Host & Microbe
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- (2013) C. A. Lozupone et al. GENOME RESEARCH
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- (2013) Lawrence A. David et al. NATURE
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- (2013) Simon Anders et al. Nature Protocols
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- (2013) Paul J. McMurdie et al. PLoS One
- Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice
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- (2013) Franck Rapaport et al. GENOME BIOLOGY
- EMPeror: a tool for visualizing high-throughput microbial community data
- (2013) Yoshiki Vázquez-Baeza et al. GigaScience
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- (2012) J Gregory Caporaso et al. ISME Journal
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- (2011) Daniela M. Witten Annals of Applied Statistics
- Evaluation of Subsampling-Based Normalization Strategies for Tagged High-Throughput Sequencing Data Sets from Gut Microbiomes
- (2011) Daniel Aguirre de Cárcer et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Measuring Subcompositional Incoherence
- (2011) Michael Greenacre Mathematical Geosciences
- Application of Two-Part Statistics for Comparison of Sequence Variant Counts
- (2011) Brandie D. Wagner et al. PLoS One
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- Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
- (2010) James H Bullard et al. BMC BIOINFORMATICS
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- (2010) P. L. Auer et al. GENETICS
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- (2010) Catherine Lozupone et al. ISME Journal
- A human gut microbial gene catalogue established by metagenomic sequencing
- (2010) Junjie Qin et al. NATURE
- QIIME allows analysis of high-throughput community sequencing data
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- Forensic identification using skin bacterial communities
- (2010) N. Fierer et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- (2010) J. G. Caporaso et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- (2009) P. D. Schloss et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
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