phyloseq

There are 3 repositories under phyloseq topic.

microbiome / microbiome
microbiome R package
microbiome microbiology microbiome-analysis r phyloseq human-microbiome population-study hitchip hitchip-atlas
Language:R 275
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.
microbiome-data color-palette microshades-cvd-palettes phyloseq cvd r data-visualization
Language:R 46
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/
bioinformatics microbiome microbiota 16s dada2 phyloseq illumina lefse picrust2
Language:R 33
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.
16s dada2 microbiome phyloseq teaching
Language:HTML 25
cafferychen777 / MicrobiomeStat
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
16s-rrna amplicon-sequencing dada2 longitudinal-data metagenomes metagenomic-analysis microbiome microbiome-analysis microbiome-data phyloseq qiime2 statistics visualization microbiome-workflow omics omics-data-integration
Language:R 24
gmteunisse / fantaxtic
Fantaxtic - Nested Bar Plots for Phyloseq Data
ggplot2 microbiome phyloseq r r-package visualization barplot multilevel nested
Language:R 24
vallenderlab / MicrobiomeR
A comprehensive and customizable R package for microbiome analysis.
microbiome microbial-genomics microbiome-analysis phyloseq metacoder r rstats visualization color-palette bioinformatics permanova alpha-diversity beta-diversity pcoa comprehensive metagenomics microbiology
Language:R 18
CenterForStatistics-UGent / RCM
A model-based visualization method for microbiome data
rcm phyloseq ordination microbiome
Language:R 16
quadram-institute-bioscience / dadaist2
Dadaist2 🟨 Highway to R
dada2 asv bioinformatics 16s amplicon-pipeline taxonomy phyloseq metabarcoding
Language:HTML 14
itsmisterbrown / microfiltR
accessory functions for processing microbial community data
microbiome microbiome-analysis marker-gene-analysis 16s phyloseq 18s
Language:R 12
erictleung / phyloseq-cheatsheet
:notebook: Minimal cheatsheet for functions in the phyloseq R package
phyloseq microbiome data-analysis cheatsheet notes r microbiota bioconductor bioinformatics
6
vaulot / R_tutorials
Tutorials for R
r phyloseq metabarcoding tutorials
Language:HTML 6
biocorecrg / microbiome_procedures
Mothur procedures for 16S and ITS analysis
microbiome-analysis microbiome-workflow 16s its mothur phyloseq fungi
Language:R 5
EmoryIntegratedComputationalCore / Methods
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
analytical-processes bayseq bioconductor comparison-groups deseq2 discovery-rates edger emory ldm methods microbiome-analysis notebook omics-experiments phyloseq qiime2 qvalue rna-seq rna-seq-analysis rna-seq-pipeline
Language:R 5
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
r phyloseq deseq2 microbiome-analysis
Language:R 4
mvuko / meta_phyloseq
How to analyze shotgun metagenomic data with phyloseq - a walkthrough
microbiome rstats phyloseq metagenomics
Language:HTML 4
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
bioinformatics microbiome microbiota 16s dada2 phyloseq illumina lefse picrust2
Language:R 4
Brochado-Kith / microbiome_analysis
The following codes are focused on microbiome analysis, alpha, beta and relative abundance differences.
16s alpha-diversity beta-diversity microbiome microbiome-analysis microbiome-workflow phyloseq rstudio shinny beta diversity metagenomic-pipeline
Language:R 3
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.
16s 16s-seq dada2 illumina illumina-sequencing metagenomics microbial-ecology microbiota phyloseq pipeline
Language:R 3
pjtorres / Bioinformatics-BC
New to Bioinformatics? Start Here!
jupyter-notebook tutorial phyloseq bioinformatics
Language:Jupyter Notebook 3
jessmhoehner / Methods
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
deseq2 edger bayseq rnaseq phyloseq 16s microbiome-analysis proteomics-data-analysis proteus ldm qvalue r metabolomics metagenomics transcriptomics-data
Language:R 2
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.
limma microbiome microbiome-analysis phyloseq
Language:R 2
nishattasnim11 / 16S_soilgut
MSc - 16S sequence datasets, amplicon analysis, and stats
qiime otu-table phyloseq ggplot2
Language:R 2
AlmaasLab / micInt
R package for analyzing microbial co-occurences
microbiome-analysis co-occurence phyloseq data-manipulation r
Language:R 1
csc-training / chipster-microbial
Microbial Community Analysis with Chipster
amplicon-sequencing bioinformatics data-analysis exercises microbiology mothur phyloseq training
1
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.
amplicon-sequencing bacteria ecology limnology microbiome paleolimnology phyloseq qiime2 computer-cluster euler heatmap pca principle-component-analysis taxonomic-assignment taxonomic-classification
Language:CSS 1
marlaux / Metabarcoding-script-by-script
Former version of METAPIPE
demultiplexing metabarcoding otu-table phyloseq pipeline taxonomy-assignment workflow
Language:Shell 1
MicrobialGenomics-IrsicaixaOrg / dar
dar: runs multiple differential abundance analysis methods and through a consensus strategy returns a set of differentially abundant features.
microbiome microbiology rstats bioconductor biomarker-discovery differential-abundance-analysis feature-selection phyloseq
Language:R 1
natmurad / amplicon16S
Analysis for amplicon data
16s amplicon metagenomics microbiome-workflow phyloseq qiime2
Language:Jupyter Notebook 1
roey-angel / Rock_weathering
Analysis scripts, data files and plots used in the manuscript
microbiome microbiology geology isotopes manuscript manuscript-figures phyloseq ggplot2 r
Language:HTML 1
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.
dada2 lefse phyloseq picrust2 python rstudio
Language:R 0
Sam-Koehler / USDA-ARS-fusarium-community
R workflows used to analyze microbial community sequence data
deseq2 fusarium microbiome microbiome-analysis otu phylogenetics phyloseq
Language:R 0
jrotzetter / metaphlanToPhyloseq
A simple R package to convert MetaPhlAn 4 output profiles to a phyloseq object.
metaphlan metaphlan4 microbiome phyloseq r
Language:R
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).
ecology metabarcoding phyloseq
Language:R
Weimar45 / Andera
En este repositorio se crearán diferentes flujos de trabajo para el análisis del microbioma con Bioconductor.
bioconductor bioinformatics microbiology microbiome-analysis phyloseq r
Language:HTML
Weimar45 / Andera-Shiny
Aplicación en Shiny del proyecto desarrollado en el repositorio Andera de análisis metagenómicos de microbiomas
bioinformatics phyloseq rstats rstudio shiny shinydashboard
Language:R

phyloseq

microbiome / microbiome

KarstensLab / microshades

ycl6 / 16S-rDNA-V3-V4

shandley / Microbiome-Analysis-Using-R

cafferychen777 / MicrobiomeStat

gmteunisse / fantaxtic

vallenderlab / MicrobiomeR

CenterForStatistics-UGent / RCM

quadram-institute-bioscience / dadaist2

itsmisterbrown / microfiltR

erictleung / phyloseq-cheatsheet

vaulot / R_tutorials

biocorecrg / microbiome_procedures

EmoryIntegratedComputationalCore / Methods

meyermicrobiolab / Stony-Coral-Tissue-Loss-Disease-SCTLD-Project

mvuko / meta_phyloseq

ycl6 / 16S-Demo

Brochado-Kith / microbiome_analysis

Headonpillow / 16S_analysis

pjtorres / Bioinformatics-BC

jessmhoehner / Methods

mucosal-immunology-lab / microbiome-analysis

nishattasnim11 / 16S_soilgut

AlmaasLab / micInt

csc-training / chipster-microbial

johannabosch / Microbiome-Analysis-Using-Clusters

marlaux / Metabarcoding-script-by-script

MicrobialGenomics-IrsicaixaOrg / dar

natmurad / amplicon16S

roey-angel / Rock_weathering

gabrielatof / tesis-mic

Sam-Koehler / USDA-ARS-fusarium-community

jrotzetter / metaphlanToPhyloseq

JustJaxz / Region-Comparison-Pipeline

Weimar45 / Andera

Weimar45 / Andera-Shiny