microsud

Tools-Microbiome-Analysis

A list of R environment based tools for microbiome data exploration, statistical analysis and visualization

microbiomeutilities

The is mostly a wrapper tool using phyloseq and microbiome R packages.

dysbiosisR

The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures

syncomR

R package with wrapped functions for synthetic microbial community analysis.

chkMocks

Check your mock communities from microbiome sequencing experiments

Db-MM-10

Synthetic gut minimal microbiome with 10-core species

Microbial-bioinformatics-introductory-course-Material-2018

Bacterial-Proteomics-in-R

BigDataBasicInsights

biomeomics

rivm toolbox

CoronaWatchNL

COVID-19 disease count cases in The Netherlands by RIVM, LCPS and NICE

datasharing

The Leek group guide to data sharing

gutmicrobe_webpage.io

ili_elderly_microbiota

jeevanuDB

Example data sets and other data type for microbiome package https://github.com/microbiome/microbiome

MDb-MM

metagenomic_binning_review

Code used to analyse and plot metadata of metagenomic binning tools

MIB20306MicrobialPhysiology

Teaching MIB20306: Interactive app created to teach proteomics guided investigation of bacterial metabolism. We use Intestinimonas butyriciproducens as example.

microbiomedatarepo

Access to few of the publicly available gut microbiome data sets as part of the microbiomeutilities R package

microbiomeDataSets

Experiment Hub based microbiome datasets

microsud

mni-website

pepper

PePPer - Personalized Perturbation Profiler

quarto_microbiome

R_for_Microbial_Ecology

Main webpage with information, tutorial, etc

Shetty_et_al_Anaerobutyricum_physiology

Codes from study on characterization of physiology of Anaerobutyricum and related species

sudarshanshetty.io

Personal Website

TeachingMIB20306

Teaching MIB20306: Interactive app created to teach proteomics guided investigation of bacterial metabolism. We use Intestinimonas butyriciproducens as example.

testFieldOpenScienceMicrobiome

urt_microbiota