WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data

[1]  R. Irizarry ggplot2 , 2019, Introduction to Data Science.

[2]  Elhanan Borenstein,et al.  BURRITO: An Interactive Multi-Omic Tool for Visualizing Taxa–Function Relationships in Microbiome Data , 2018, Front. Microbiol..

[3]  Igor Goryanin,et al.  ASAR: visual analysis of metagenomes in R , 2017, Bioinform..

[4]  Curtis Huttenhower,et al.  bioBakery: a meta’omic analysis environment , 2017, Bioinform..

[5]  A. Milstone,et al.  Manipulating the Microbiome: Evolution of a Strategy to Prevent S. aureus Disease in Children , 2017, Journal of Perinatology.

[6]  Xiao Guo,et al.  MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics , 2017, BMC Bioinformatics.

[7]  Niklas Elmqvist,et al.  Metaviz: interactive statistical and visual analysis of metagenomic data , 2017, bioRxiv.

[8]  Paolo Manghi,et al.  Accessible, curated metagenomic data through ExperimentHub , 2017, Nature Methods.

[9]  Raju V. Misra,et al.  Antibiotic resistance potential of the healthy preterm infant gut microbiome , 2017, PeerJ.

[10]  Dmitry Alexeev,et al.  Methods for The Metagenomic Data Visualization and Analysis. , 2017, Current issues in molecular biology.

[11]  D. Alexeev,et al.  Guidelines to Statistical Analysis of Microbial Composition Data Inferred from Metagenomic Sequencing. , 2017, Current issues in molecular biology.

[12]  Yi Wang,et al.  MetaCoMET: a web platform for discovery and visualization of the core microbiome , 2016, Bioinform..

[13]  Paul J. McMurdie,et al.  DADA2: High resolution sample inference from Illumina amplicon data , 2016, Nature Methods.

[14]  Danielle G. Lemay,et al.  SAMSA: a comprehensive metatranscriptome analysis pipeline , 2016, bioRxiv.

[15]  Elizabeth M Glass,et al.  MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function. , 2016, Methods in molecular biology.

[16]  Duy Tin Truong,et al.  MetaPhlAn2 for enhanced metagenomic taxonomic profiling , 2015, Nature Methods.

[17]  Shili Lin,et al.  GrammR: graphical representation and modeling of count data with application in metagenomics , 2015, Bioinform..

[18]  T. Lumley,et al.  gplots: Various R Programming Tools for Plotting Data , 2015 .

[19]  A. Butte,et al.  The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease , 2014, Cell host & microbe.

[20]  A. Murat Eren,et al.  VAMPS: a website for visualization and analysis of microbial population structures , 2014, BMC Bioinformatics.

[21]  Rob Knight,et al.  EMPeror: a tool for visualizing high-throughput microbial community data , 2013, GigaScience.

[22]  Jean M. Macklaim,et al.  ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq , 2013, PloS one.

[23]  Daniel H Huson,et al.  Microbial community analysis using MEGAN. , 2013, Methods in enzymology.

[24]  William A. Walters,et al.  Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities , 2012, Current protocols in microbiology.

[25]  Bernard Henrissat,et al.  Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome , 2012, PLoS Comput. Biol..

[26]  Katherine H. Huang,et al.  Structure, Function and Diversity of the Healthy Human Microbiome , 2012, Nature.

[27]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[28]  Martin Hartmann,et al.  Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.

[29]  S. Kravitz,et al.  CAMERA: A Community Resource for Metagenomics , 2007, PLoS biology.

[30]  T. Muir,et al.  Virulence gene regulation by peptides in staphylococci and other Gram-positive bacteria. , 1999, Current opinion in microbiology.

[31]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .