zaidissa

Freyja

Depth-weighted De-Mixing

FriendsDontLetFriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

decontam

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

ControllingContaminants16S

oakvar

Genomic variant analysis platform

amplicon

Statistics and visualization for amplicon data

analysis_of_microbiome_community_data_in_r

This is the source code for the "Analysis of Microbiome Community Data in R" ICPP 2018 workshop. The website is available at: https://grunwaldlab.github.io/analysis_of_microbiome_community_data_in_r/

Tools-Microbiome-Analysis

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

EasyAmplicon

Easy Amplicon data analysis pipeline

EasyMetagenome

Easy Metagenome Pipeline

atlas

ATLAS - Three commands to start analyzing your metagenome data

CAMISIM

CAMISIM: Simulating metagenomes and microbial communities

metagenome-analysis

Strain-Level_Metagenome_Analysis

Using a universal reference database, mixed assemblies, and cutting-edge software to give you the quantitative community phylogeny, a complete community functional analysis, and many strain(ish)-level high-quality bins.

eQTLQC

brainMicrobiomeRscripts

Scripts for brain microbiome analysis

MicrobiomeBestPracticeReview

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing