Biocview "Microbiome"

Accurate, high-resolution sample inference from amplicon sequencing data

A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

A lecture on sequence count data

A metagenomic pipeline for systems biology

Analysis for short time-series data

Analysis of compositions of microbiomes with bias correction

Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

Analysis Of Differential Abundance Taking Sample Variation Into Account

Analyze Microbiome Data

An interface package for the BIOM file format

an R package for analysis, visualization and biomarker discovery of microbiome

An R/shiny package for microbiome functional enrichment analysis

A Statistical Model for Describing and Simulating Microbial Community Profiles

Benchmark of differential abundance methods on microbiome data

Compare Characteristic Features of Count Data Sets

Comparing Differential Abundance/Expression Methods

Competitive Balances for Taxonomic Enrichment Analysis in R

Compositional omics model based visual integration

Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data

Easy Use R

Evaluation and correction of batch effects in microbiome data-sets

Exploration of marker-gene sequence taxonomic annotations

FASTQ2OTU: Automate microbiome analyses

Feature-Wise Normalization for Microbiome Sequencing Data

Find microbial interactions

Fit row-column association models with the negative binomial distribution for the microbiome

Functions to help analyze data as phyloseq objects

Generalized correlation analysis and model construction strategy for metabolome and microbiome

Greengenes 13.5 16S rRNA Database Annotation Data

Greengenes 13.8 85% similarity OTU threshold 16S rRNA Database Annotation Data

Greengenes 13.8 88% similarity OTU threshold 16S rRNA Database Annotation Data

Greengenes 13.8 91% similarity OTU threshold 16S rRNA Database Annotation Data

Greengenes 13.8 94% similarity OTU threshold 16S rRNA Database Annotation Data

Greengenes 13.8 97% similarity OTU threshold 16S rRNA Database Annotation Data

Handling and analysis of high-throughput microbiome census data

Identify Contaminants in Marker-gene and Metagenomics Sequencing Data

Integrative analysis of the microbiome and metabolome

Interactive microbiome analysis toolkit

Interface to the RDP Classifier

Maaslin2

Mapping of Phyloseq Information

Meta-analysis for the metagenomic read counts data from different cohorts

Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies

Metabarcoding and microbiome analysis using multiple amplicons

Microbiome analysis

Microbiome Analysis Plotting and Visualization

Microbiome Analytics

microbiome biomarker analysis toolkit

Microbiome Data Simulation

Microbiome differential abudance and correlation analyses with bias correction

Microbiome Differential Abundance Simulation

Microbiome Exploration App

Microbiome Time Series Analysis

Miscellaneous Functions for Metabarcoding Analysis

Multimodal Mediation Analysis

"Multivariable Association Discovery in Population-scale Meta-omics Studies"

Omics Longitudinal Differential Analysis

PathoStat Statistical Microbiome Analysis Package

Permutation filtration for microbiome data

Phylogenetic partitioning based ILR transform for metagenomics data

PLSDA-batch

Professional Comprehensive Omics Data Analysis

qiime2R

Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities

Resampling Collapsed Null Distributions for Simultaneous Inference

Ribosomal Database Project 16S rRNA release 11.5 Annotation Data

R implementation of the LEfSE method for microbiome biomarker discovery

Robust Inference for Absolute Abundance in Microbiome Analysis

R-side access to published microbial signatures from BugSigDB

SILVA SSR rRNA release 128.1 Annotation Data

Sparse Data Observations for Simulating Synthetic Abundance

Statistical analysis for sparse high-throughput sequencing

Statistical approaches for differential expression analysis in metatranscriptomics

Statistical Inference of Associations between Microbial Communities And host phenoTypes

Tools for curating, analyzing, and manipulating biological sequences

Tools for microbiome analysis

Tree Aggregation

Visual Exploration of Omic Datasets Using a Shiny App

visualization and interpretation of textual information from omics summary data through network analysis

Biocview "Microbiome"

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