Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox

References

Page 1

	Year	Citations
Regression Shrinkage and Selection Via the Lasso Robert Tibshirani Journal of the Royal Statistical Society Series B (Statistical Methodology) EngineeringHigh-dimensional MethodRobust ModelingEstimation StatisticFeature Selection	1996	50.3K
DADA2: High-resolution sample inference from Illumina amplicon data Benjamin J. Callahan, Paul J. McMurdie, Michael Rosen, Nature Methods Illumina Amplicon DataOmics DatasetsSpectral SearchingOmicsBiostatistics	2016	33.5K
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data Paul J. McMurdie, Susan Holmes PLoS ONE	2013	21K
Regularization and Variable Selection Via the Elastic Net Hui Zou, Trevor Hastie Journal of the Royal Statistical Society Series B (Statistical Methodology)	2005	20.1K
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy Qiong Wang, George M Garrity, James M. Tiedje, Applied and Environmental Microbiology	2007	20K
Metagenomic biomarker discovery and explanation Nicola Segata, Jacques Izard, Levi Waldron, Genome biology	2011	15.8K
A core gut microbiome in obese and lean twins Peter J. Turnbaugh, Micah Hamady, Tanya Yatsunenko, Nature ObesityNutritionDysbiosisMicrobiotaGut Microbiology	2008	7.8K
A metagenome-wide association study of gut microbiota in type 2 diabetes Junjie Qin, Yingrui Li, Zhiming Cai, Nature DysbiosisMicrobiotaDiabetesGut MicrobiologyType 2	2012	6.7K
Random decision forests Tin Kam Ho EngineeringMachine LearningGeneralization AccuracyClassification MethodData Science	2002	4.9K
Richness of human gut microbiome correlates with metabolic markers Emmanuelle Le Chatelier, Trine Nielsen, Junjie Qin, Nature DysbiosisMedicineMicrobiotaGut MicrobiologyHuman Microbial Flora	2013	4.6K

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