phyloseq
There are 44 repositories under phyloseq topic.
microbiome/microbiome
microbiome R package
KarstensLab/microshades
This repo contains the R microshades package, which contains a color blind accessible color palette with 30 unique colors and functions for applying these colors to microbiome data.
ycl6/16S-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/
cafferychen777/MicrobiomeStat
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
gmteunisse/fantaxtic
Fantaxtic - Nested Bar Plots for Phyloseq Data
shandley/Microbiome-Analysis-Using-R
Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.
vallenderlab/MicrobiomeR
A comprehensive and customizable R package for microbiome analysis.
CenterForStatistics-UGent/RCM
A model-based visualization method for microbiome data
quadram-institute-bioscience/dadaist2
Dadaist2 🟨 Highway to R
itsmisterbrown/microfiltR
accessory functions for processing microbial community data
erictleung/phyloseq-cheatsheet
:notebook: Minimal cheatsheet for functions in the phyloseq R package
vaulot/R_tutorials
Tutorials for R
biocorecrg/microbiome_procedures
Mothur procedures for 16S and ITS analysis
EmoryIntegratedComputationalCore/Methods
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
mvuko/meta_phyloseq
How to analyze shotgun metagenomic data with phyloseq - a walkthrough
meyermicrobiolab/Stony-Coral-Tissue-Loss-Disease-SCTLD-Project
R scripts used for the analysis of microbiomes associated with stony coral tissue loss disease (SCTLD) in the Florida Reef Tract
ycl6/16S-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
Brochado-Kith/microbiome_analysis
The following codes are focused on microbiome analysis, alpha, beta and relative abundance differences.
Headonpillow/16S_analysis
A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.
pjtorres/Bioinformatics-BC
New to Bioinformatics? Start Here!
jessmhoehner/Methods
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
mucosal-immunology-lab/microbiome-analysis
A selection of analytical approaches, tools, and utilities for the processing of microbiome data derived from either 16S rRNA amplicon sequencing or shotgun metagenomics.
nishattasnim11/16S_soilgut
MSc - 16S sequence datasets, amplicon analysis, and stats
AlmaasLab/micInt
R package for analyzing microbial co-occurences
csc-training/chipster-microbial
Microbial Community Analysis with Chipster
johannabosch/Microbiome-Analysis-Using-Clusters
This is a 16S amplicon analysis for visualizing microbiome data using QIIME, QIIME2R and Phyloseq. DNA was isolated fom both sediment cores and seabird fecal samples for this analysis.
marlaux/Metabarcoding-script-by-script
Former version of METAPIPE
MicrobialGenomics-IrsicaixaOrg/dar
dar: runs multiple differential abundance analysis methods and through a consensus strategy returns a set of differentially abundant features.
natmurad/amplicon16S
Analysis for amplicon data
roey-angel/Rock_weathering
Analysis scripts, data files and plots used in the manuscript
gabrielatof/tesis-mic
En este repositorio se encuentran todos los scripts utilizados para mi tesis de licenciatura, titulada: "Análisis de perfiles funcionales de la microbiota intestinal de pacientes con trastorno depresivo mayor", la cual utiliza un lenguaje de programación en R y Phyton.
Sam-Koehler/USDA-ARS-fusarium-community
R workflows used to analyze microbial community sequence data
jrotzetter/metaphlanToPhyloseq
A simple R package to convert MetaPhlAn 4 output profiles to a phyloseq object.
JustJaxz/Region-Comparison-Pipeline
Scripts used to analyse metabarcoding data from two different gene regions to assess which provides a more complete picture of the eukaryotic marine microalgae community (EMC).
Weimar45/Andera
En este repositorio se crearán diferentes flujos de trabajo para el análisis del microbioma con Bioconductor.
Weimar45/Andera-Shiny
Aplicación en Shiny del proyecto desarrollado en el repositorio Andera de análisis metagenómicos de microbiomas