Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: phyloseq
cafferychen777/MicrobiomeStat
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
Language: R - Size: 15.7 MB - Last synced: about 8 hours ago - Pushed: 2 days ago - Stars: 24 - Forks: 3
marlaux/Metabarcoding-script-by-script
Former version of METAPIPE
Language: Shell - Size: 12.9 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 1 - Forks: 0
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.
Language: R - Size: 23 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 46 - Forks: 10
jrotzetter/metaphlanToPhyloseq
A simple R package to convert MetaPhlAn 4 output profiles to a phyloseq object.
Language: R - Size: 2.88 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0
microbiome/microbiome
microbiome R package
Language: R - Size: 392 MB - Last synced: 19 days ago - Pushed: 10 months ago - Stars: 273 - Forks: 56
MicrobialGenomics-IrsicaixaOrg/dar
dar: runs multiple differential abundance analysis methods and through a consensus strategy returns a set of differentially abundant features.
Language: R - Size: 38.5 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 1 - Forks: 0
csc-training/chipster-microbial
Microbial Community Analysis with Chipster
Size: 2.59 MB - Last synced: 2 months ago - Pushed: 8 months ago - Stars: 1 - Forks: 1
Brochado-Kith/microbiome_analysis
The following codes are focused on microbiome analysis, alpha, beta and relative abundance differences.
Language: R - Size: 1.34 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 3 - Forks: 0
joeweaver/get_to_know_phyloseq
An interactive Jupyter-based tutorial prepared for the de los Reyes lab, interested colleagues, and the North Carolina State University BIT 477/577 Metagenomics course
Language: Jupyter Notebook - Size: 690 KB - Last synced: 3 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0
erictleung/phyloseq-cheatsheet
:notebook: Minimal cheatsheet for functions in the phyloseq R package
Size: 504 KB - Last synced: 15 days ago - Pushed: about 3 years ago - Stars: 6 - Forks: 0
quadram-institute-bioscience/dadaist2
Dadaist2 🟨 Highway to R
Language: HTML - Size: 39.4 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 13 - Forks: 5
Weimar45/Andera
En este repositorio se crearán diferentes flujos de trabajo para el análisis del microbioma con Bioconductor.
Language: HTML - Size: 134 MB - Last synced: 4 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0
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.
Language: R - Size: 70.3 KB - Last synced: 4 months ago - Pushed: 5 months ago - Stars: 3 - Forks: 0
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.
Language: R - Size: 1.6 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 0
xvtyzn/nyankomicro
nyankomicro is a in-house package that aims to make the plots more beautiful.
Language: R - Size: 1.16 MB - Last synced: 6 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
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/
Language: R - Size: 309 KB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 27 - Forks: 17
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.
Language: HTML - Size: 32.4 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 22 - Forks: 23
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
Language: R - Size: 1.93 GB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 4 - Forks: 0
gmteunisse/fantaxtic
Fantaxtic - Nested Bar Plots for Phyloseq Data
Language: R - Size: 1.17 MB - Last synced: 7 months ago - Pushed: 11 months ago - Stars: 19 - Forks: 2
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.
Language: R - Size: 634 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 1
pjtorres/Bioinformatics-BC
New to Bioinformatics? Start Here!
Language: Jupyter Notebook - Size: 15.4 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 2 - Forks: 2
nishattasnim11/16S_soilgut
MSc - 16S sequence datasets, amplicon analysis, and stats
Language: R - Size: 443 KB - Last synced: 8 months ago - Pushed: about 5 years ago - Stars: 2 - Forks: 0
jessmhoehner/Methods Fork of EmoryIntegratedComputationalCore/Methods
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
Language: R - Size: 18 MB - Last synced: 9 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0
microsud/Gut-microbiota-Celiac-disease
R scripts used for analysis of data reported in Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Patients with Celiac Disease and Controls
Language: HTML - Size: 1.56 MB - Last synced: 10 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0
Weimar45/Andera-Shiny
Aplicación en Shiny del proyecto desarrollado en el repositorio Andera de análisis metagenómicos de microbiomas
Language: R - Size: 1.15 MB - Last synced: 4 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0
natmurad/amplicon16S
Analysis for amplicon data
Language: Jupyter Notebook - Size: 134 KB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
vaulot/R_tutorials
Tutorials for R
Language: HTML - Size: 31.4 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 6 - Forks: 5
roey-angel/Rock_weathering
Analysis scripts, data files and plots used in the manuscript
Language: HTML - Size: 56.4 MB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 1 - Forks: 0
CenterForStatistics-UGent/RCM
A model-based visualization method for microbiome data
Language: R - Size: 24.3 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 16 - Forks: 2
vallenderlab/MicrobiomeR
A comprehensive and customizable R package for microbiome analysis.
Language: R - Size: 18.8 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 18 - Forks: 3
biocorecrg/microbiome_procedures
Mothur procedures for 16S and ITS analysis
Language: R - Size: 124 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 3 - Forks: 6
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
Language: R - Size: 27.8 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 4 - Forks: 3
EmoryIntegratedComputationalCore/Methods
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
Language: R - Size: 18 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 5 - Forks: 2
AlmaasLab/micInt
R package for analyzing microbial co-occurences
Language: R - Size: 747 KB - Last synced: 7 months ago - Pushed: about 2 years ago - Stars: 2 - Forks: 0
itsmisterbrown/microfiltR
accessory functions for processing microbial community data
Language: R - Size: 3.84 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 12 - Forks: 11
Sam-Koehler/USDA-ARS-fusarium-community
R workflows used to analyze microbial community sequence data
Language: R - Size: 205 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0
shandley/human_volunteer_rotabiome
Analysis of 16S rRNA (dada2 amplicon sequence variants) from human volunteers given various vaccines following two different antibiotics treatments compared to no antibiotics.
Language: HTML - Size: 31.7 MB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 5
meyermicrobiolab/Microbiomes-of-nursery-reared-Acropora-cervicornis
R scripts used for the analysis of microbiomes of nursery-reared Acropora cervicornis
Language: R - Size: 2.29 GB - Last synced: 12 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0
erictleung/shinySampleSelect
:fishing_pole_and_fish: Quick Shiny application to help triage multiple samples from subjects
Language: R - Size: 3.91 KB - Last synced: 15 days ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0
megaptera-helvetiae/SalmoTruttaVals
Analysis of Salmo trutta gametes and embryo microbiome project in Vals/Trun, Switzerland
Language: R - Size: 1.23 MB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0
