Normalization and microbial differential abundance strategies depend upon data characteristics

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Normalization and microbial differential abundance strategies depend upon data characteristics is …
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scholarly articleQ13442814

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P6179Dimensions Publication ID1084252802
P356DOI10.1186/S40168-017-0237-Y
P2888exact matchhttps://scigraph.springernature.com/pub.10.1186/s40168-017-0237-y
P932PMC publication ID5335496
P698PubMed publication ID28253908

P50authorRob KnightQ20657126
Catherine A. LozuponeQ21425018
Shyamal D PeddadaQ56448445
Amnon AmirQ89259798
Kyle BittingerQ91874782
Amanda BirminghamQ92172536
Zhenjiang Zech XuQ110853861
Yoshiki Vázquez-BaezaQ110853916
Antonio GonzalezQ110864255
Embriette R HydeQ110875315
P2093author name stringJesse R Zaneveld
Sophie Weiss
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Saliva from obese individuals suppresses the release of aroma compounds from wineQ28538972
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Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample sizeQ40105344
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Bayesian inference for categorical data analysisQ55884938
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zCompositions — R package for multivariate imputation of left-censored data under a compositional approachQ58002985
Bayesian-multiplicative treatment of count zeros in compositional data setsQ58002986
UniFrac: a new phylogenetic method for comparing microbial communitiesQ29547435
Diet rapidly and reproducibly alters the human gut microbiomeQ29547454
Count-based differential expression analysis of RNA sequencing data using R and BioconductorQ29577114
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experimentsQ29614452
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platformsQ29614454
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sampleQ29614456
Gut microbiota from twins discordant for obesity modulate metabolism in miceQ29614796
Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scaleQ29617333
Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota compositionQ30412052
A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysisQ30567356
Inferring correlation networks from genomic survey dataQ30571637
Hypothesis testing and power calculations for taxonomic-based human microbiome dataQ30584286
EMPeror: a tool for visualizing high-throughput microbial community dataQ30702273
VARIABLE SELECTION FOR SPARSE DIRICHLET-MULTINOMIAL REGRESSION WITH AN APPLICATION TO MICROBIOME DATA ANALYSIS.Q30709584
Zero-inflated models for regression analysis of count data: a study of growth and developmentQ30714487
Waste not, want not: why rarefying microbiome data is inadmissibleQ30793257
Estimating coverage in metagenomic data sets and why it mattersQ30819837
Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysisQ30829889
A taxa-area relationship for bacteriaQ33209794
Small-sample estimation of negative binomial dispersion, with applications to SAGE dataQ33295482
Statistical methods for detecting differentially abundant features in clinical metagenomic samplesQ33429043
Differential abundance analysis for microbial marker-gene surveysQ33566352
Statistical design and analysis of RNA sequencing dataQ33571320
voom: Precision weights unlock linear model analysis tools for RNA-seq read countsQ33741687
The treatment-naive microbiome in new-onset Crohn's diseaseQ33762817
Forensic identification using skin bacterial communitiesQ33778976
Application of two-part statistics for comparison of sequence variant countsQ33918415
Evaluation of subsampling-based normalization strategies for tagged high-throughput sequencing data sets from gut microbiomesQ34044569
Evaluating bias of illumina-based bacterial 16S rRNA gene profilesQ34261037
A comparison of methods for differential expression analysis of RNA-seq dataQ34333243
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq dataQ34369969
Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communitiesQ34601325
Meta-analyses of studies of the human microbiotaQ34824829
Alterations in the gut microbiota associated with HIV-1 infectionQ34986967
UniFrac: an effective distance metric for microbial community comparisonQ35018645
Analysis of composition of microbiomes: a novel method for studying microbial compositionQ35668886
Testing species abundance models: a new bootstrap approach applied to Indo-Pacific coral reefsQ38951788
P4510describes a project that usesDESeq2Q113018293
edgeRQ113334690
P433issue1
P304page(s)27
P577publication date2017-03-03
P1433published inMicrobiomeQ27725102
P1476titleNormalization and microbial differential abundance strategies depend upon data characteristics
P478volume5

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