[HTML][HTML] phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data
PJ McMurdie, S Holmes�- PloS one, 2013 - journals.plos.org
Background The analysis of microbial communities through DNA sequencing brings many
challenges: the integration of different types of data with methods from ecology, genetics�…
challenges: the integration of different types of data with methods from ecology, genetics�…
[HTML][HTML] VAMPS: a website for visualization and analysis of microbial population structures
SM Huse, DB Mark Welch, A Voorhis, A Shipunova…�- BMC�…, 2014 - Springer
Background The advent of next-generation DNA sequencing platforms has revolutionized
molecular microbial ecology by making the detailed analysis of complex communities over�…
molecular microbial ecology by making the detailed analysis of complex communities over�…
[PDF][PDF] microViz: an R package for microbiome data visualization and statistics
DJM Barnett, ICW Arts, J Penders�- Journal of Open Source Software, 2021 - joss.theoj.org
Summary microViz is an R package for the statistical analysis and visualization of microbiota
data. This package extends the functionality of popular microbial ecosystem data analysis R�…
data. This package extends the functionality of popular microbial ecosystem data analysis R�…
[PDF][PDF] MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data
The widespread application of next-generation sequencing technologies has revolutionized
microbiome research by enabling high-throughput profiling of the genetic contents of�…
microbiome research by enabling high-throughput profiling of the genetic contents of�…
Microbiome helper: a custom and streamlined workflow for microbiome research
Sequence-based approaches to study microbiomes, such as 16S rRNA gene sequencing
and metagenomics, are uncovering associations between microbial taxa and a myriad of�…
and metagenomics, are uncovering associations between microbial taxa and a myriad of�…
ampvis2: an R package to analyse and visualise 16S rRNA amplicon data
Microbial community analysis using 16S rRNA gene amplicon sequencing is the backbone
of many microbial ecology studies. Several approaches and pipelines exist for processing�…
of many microbial ecology studies. Several approaches and pipelines exist for processing�…
[HTML][HTML] Introduction to the microbiome R package
This vignette provides a brief overview with example data sets from published microbiome
profiling studies (Lahti et al. 2014, Lahti et al.(2013), O'Keefe et al.(2015)). A more�…
profiling studies (Lahti et al. 2014, Lahti et al.(2013), O'Keefe et al.(2015)). A more�…
[PDF][PDF] phylosmith: an R-package for reproducible and efficient microbiome analysis with phyloseq-objects
S Smith�- Journal of Open Source Software, 2019 - par.nsf.gov
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Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data
Studies of the human microbiome, and microbial community ecology in general, have
blossomed of late and are now a burgeoning source of exciting research findings. Along�…
blossomed of late and are now a burgeoning source of exciting research findings. Along�…
[HTML][HTML] Bioconductor workflow for microbiome data analysis: from raw reads to community analyses
High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene)
has enabled a new level of analysis of complex bacterial communities known as�…
has enabled a new level of analysis of complex bacterial communities known as�…