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16s-demo

Working Demo on 16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Visit repo website for HTML output

16s-rdna-v3-v4

16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/

ampliseq

16S rRNA amplicon sequencing analysis workflow using QIIME2

ancom

R scripts for Analysis of Composition of Microbiomes (ANCOM).

astrobiomike.github.io

Site to help biologists wade their way into bioinformatics.

canutrients

Canadian Nutrient File 2015 data in a R package

cbmbtools

General purpose package containing useful functions for microbiome analysis pipelines

datest

Compare different differential abundance and expression methods

dietaryindex

R Package for Calculating Healthy Eating Index (HEI), Alternative Healthy Eating Index (AHEI), Dietary Approaches to Stop Hypertension (DASH), Mediterranean Diet (MED), Dietary Inflammation Index (DII) for the NHANES, ASA24, DHQ, and other dietary assessments

dietstudy_analyses

enrichplot

Visualization of Functional Enrichment Result

food_tree

USDA Nutrition codes Tree

gage

Generally Applicable Gene-set Enrichment for Pathway Analysis

humann

HUMAnN 3.0 is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

introduction-to-metagenomics-summer-workshop-2019

Data, scripts, and lectures for the Introduction to Metagenomics Summer Workshop 2019.

kegg_http_tools

Query KEGG for pathways from KEGG Orthologs (KOs).

lp-diet

Linear Programming Diet Experiments

maaslin2

MaAsLin2: Microbiome Multivariate Association with Linear Models

metamicrobiomer

An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studies using random effects models

miceco

Various functions for analysis of microbial community data

microbiome

microbiome R package

microbiome-analysis-using-r

Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.

microbiome_helper

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.

microbiomeexplorer

The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or through a Shiny application. Written by Janina Reeder and Joseph N. Paulson.

microbiomemarker

R package for microbiome biomarker discovery

microbiomeviz

Visualize microbiome data with black magic ggtree

mmuphin

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

mmvec

Neural networks for microbe-metabolite interaction analysis

monai

AI Toolkit for Healthcare Imaging

nutrient_calculator

Code for a shinyapp that calculates nutrition values for food and recipes