cafferychen777/MicrobiomeStat

Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

Language: R - Size: 122 MB - Last synced at: about 9 hours ago - Pushed at: about 10 hours ago - Stars: 41 - Forks: 5

nf-core/ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Language: Nextflow - Size: 16.6 MB - Last synced at: about 18 hours ago - Pushed at: about 18 hours ago - Stars: 200 - Forks: 135

mghotbi/DspikeIn

The importance of converting relative to absolute abundance in the context of microbial ecology: Introducing the user-friendly DspikeIn R package

Language: R - Size: 59.9 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 12 - Forks: 3

gabrielatof/tesis-maestria

En este repositorio se encuentran todos los scripts utilizados para mi tesis de maestría, titulada: "Estudio in silico de la interacción metabólica entre cáncer de mama y microbiota intratumoral"

Language: Python - Size: 11.7 KB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 0 - Forks: 0

biocore/empress

A fast and scalable phylogenetic tree viewer for microbiome data analysis

Language: JavaScript - Size: 45.8 MB - Last synced at: 2 days ago - Pushed at: 9 months ago - Stars: 53 - Forks: 31

colinbrislawn/q2-forums

Colin's notes for Qiime2 forums questions

Language: HTML - Size: 3.27 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

micom-dev/q2-micom

A Qiime plugin for MICOM.

Language: Python - Size: 67.6 MB - Last synced at: 10 days ago - Pushed at: about 2 months ago - Stars: 10 - Forks: 5

jvtarss/ccm-2024

TEIXEIRA, J. V. A.; SOUZA, E. C. Use of microbial fuel cell systems in wastewater treatment in connection with bioenergy generation. Desafios. Revista Interdisciplinar da Universidade Federal do Tocantins. Palmas, 2025. DOI: // Microbial fuel cells: Unveiling microbial diversity for sustainable wastewater treatment and bioenergy production

Language: Python - Size: 95.5 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 1

biocore/gemelli

Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.

Language: Python - Size: 136 MB - Last synced at: 22 days ago - Pushed at: 7 months ago - Stars: 80 - Forks: 18

caporaso-lab/q2-boots

q2-boots: bootstrapped and rarefaction-based alpha and beta diversity analyses 🥾

Language: Python - Size: 2.69 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 3 - Forks: 6

gibsramen/evident_

Effect size calculations for microbiome data

Language: Python - Size: 1.38 MB - Last synced at: 24 days ago - Pushed at: almost 3 years ago - Stars: 5 - Forks: 1

sbslee/dokdo

A Python package for microbiome sequencing analysis with QIIME 2

Language: Python - Size: 11.9 MB - Last synced at: 23 days ago - Pushed at: about 1 year ago - Stars: 44 - Forks: 11

minuka819/BeeProjectMetagenomics

Detection of Phyto and Bee Pathogens in Bee Samples in Canada

Size: 47.7 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

Rounge-lab/skin_microbiome_16S_seq_analyses

This repository contains code for pre-processing and analysis of 16S rRNA data used to generate results in the paper "Skin bacterial community dynamics of hands and forearms before and after military field exercise".

Language: R - Size: 176 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

SergioAlias/sporeflow

🦠 SporeFlow: ITS and 16S metataxonomics pipeline

Language: Python - Size: 167 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

grigsbyanthony/msu-decomp-ms

A collection of code used in the analysis and visualization of 16S sequencing data (among other things) @ Michigan State University over the course of my master's degree.

Language: R - Size: 74.9 MB - Last synced at: 5 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

bioinfonupeb/redemicro-ana-flavia-nutri

Metagenomic analysis of the project: "PROGRAMAÇÃO METABÓLICA INDUZIDA PELA SUPERLACTAÇÃO E SEUS EFEITOS NA ATIVAÇÃO DO INFLAMASSOMA NLRP3 E EXPRESSÃO DO MIR-155 EM MODELO EXPERIMENTAL DE RESISTÊNCIA À INSULINA"

Language: Jupyter Notebook - Size: 247 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 2 - Forks: 0

noriakis/q2-pathway

QIIME 2 plugin for analyzing biological pathway information based on gene family abundances

Language: Python - Size: 289 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0

Antonionavarrorubira/16S-rRNA-data-analysis

16S rRNA sequencing data analysis of mice fed with pectin-based prebiotic fiber using both QIIME2 and R.

Language: R - Size: 7.93 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

meeranhussain/Microbiome_analysis

Comparative study of soil microbiome using QIIME2

Size: 16.6 KB - Last synced at: about 2 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

telatin/qax

Qiime2 Artifact eXtractor

Language: Nim - Size: 15.3 MB - Last synced at: 2 months ago - Pushed at: 10 months ago - Stars: 5 - Forks: 1

leylabmpi/qiime_2_ll_quick_viewer

Language: Python - Size: 75.2 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 3 - Forks: 2

StephRut/MSI-QIIME2-Pipeline-Tutorial

Language: HTML - Size: 266 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

TessaBeaver/TBeaver-G-childressi-microbiome-analysis

Microbial community dynamics during key life-history transitions in the chemosymbiotic mussel, Gigantidas childressi

Language: R - Size: 17.6 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

FranckLejzerowicz/microbiome_analyzer

Command line tool that writes commands to run one by one to perform analyses (mainly using qiime2) on a HPC running Slurm, Torque or none of these.

Language: Python - Size: 2.34 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

segrelab/MiCoNE-pipeline-paper

The source code for the MIND pipeline paper

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Metu-O/Feature-Selection-Qiime2 Fork of caporaso-lab/tax-credit-data

This repository describes the methods used to test different sci-kit learn feature selection methods as part of Qiime2 q2-classifier. It also contains raw data from the tax-credit project.

Language: Jupyter Notebook - Size: 652 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

Gibbons-Lab/isb_course_2023

Materials and presentation for the 2023 ISB Microbiome course.

Language: Jupyter Notebook - Size: 245 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 15 - Forks: 7

olabiyi/snakemake-workflow-qiime2

Snakemake pipeline for 16S, 18S and ITS metagenomics using qiime2

Language: Python - Size: 447 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 10 - Forks: 2

ohmeta/qiimepi

Snakemake version of QIIME2

Language: Python - Size: 163 KB - Last synced at: 7 days ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

DavideScarpetta/taxonomic_profiling

Metabarcoding analysis pipeline, using DADA2 and qiime2

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Gibbons-Lab/isb_course_2022

Materials and presentation for the 2022 ISB Microbiome course.

Language: Jupyter Notebook - Size: 258 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 23 - Forks: 8

yjiakang/amplicon

amplicon pipeline

Language: Shell - Size: 5.13 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

focussash/MiCoMo-Manuscript

Files for the MiCoMo project and manuscript

Language: C++ - Size: 2.54 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

Elcornevic/metaRdum

Welcome to 'Metagenomics in R for Dummies'! Are you interested in learning the essentials of metagenomics in a short period of time? You've reached the right repos!

Language: R - Size: 10.1 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

biota-inc/q2-shared_asv

q2-shared_asv is a QIIME 2 plugin for shared ASV analysis.

Language: Python - Size: 44.9 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1

Metu-O/Feature-Selection-Qiime2-

This repository describes the methods used to test different sci-kit learn feature selection methods as part of Qiime2 q2-classifier.

Language: Jupyter Notebook - Size: 9.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

PlantGGHLab/qiime2-nf

Microbiome analysis with QIIME2

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HSapers/q2-decontam

qiime2 decontam plugin

Language: Python - Size: 1.87 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 3

rjstevick/loperamide-zebrafish-dysbiosis

Analysis of 16S rRNA and in vitro data from larval zebrafish with loperamide treatment

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nezapajek/proteus-skin-microbiome

Amplicon sequencing data analysis of skin microbiota in the black olm subspecies using Qiime2

Language: Jupyter Notebook - Size: 58 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

rjstevick/PJnitrogenOysterMicrobiomes

Study of farmed oysters and nitrogen cycling in Point Judith Pond, RI. Scripts for analysis of 16S rRNA amplicon and metatranscriptomic data.

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sPuntinG/Galaxea_Microbiome_PCI

Code and raw data for *Galaxea fascicularis* microbiome data analysis

Language: R - Size: 11.9 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

SharuPaul/Metagenomics

Data analysis using QIIME2

Size: 78.4 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 2

rjstevick/NBayTNCoystersAnalysis

Scripts for analysis of metatranscriptomic and 16S rRNA amplicon data from wild oysters in Narragansett Bay

Language: R - Size: 21.8 MB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 1

natmurad/amplicon16S

Analysis for amplicon data

Language: Jupyter Notebook - Size: 134 KB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

Zubair2021/16S_Microbiome_Analysis

This repository provides scripts for the 16S microbiome analysis and metagenome prediction using linux and R-Studio

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rjstevick/zebrafish-conv-mix9-models

Analysis of 16S rRNA and microscopy data from larval zebrafish

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valentynbez/spatial_sinus_microbiome

Code for the paper "Spatial variability of the microbiome in chronic rhinosinusitis is associated with the patients’ clinical characteristics but not with sinus ostia occlusion" by Szaleniec et al. 2022

Language: Jupyter Notebook - Size: 4.42 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

bioinfonupeb/redemicro-miliane-nutri

EXPOSIÇÃO AGUDA AO CHUMBO E SUA RELAÇÃO COM ALTERAÇÕES NO STATUS REDOX E DISBIOSE INTESTINAL EM RATOS

Language: Jupyter Notebook - Size: 24.8 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

bokulich-lab/q2-protein-pca

QIIME2 plugin for PCA analysis of protein sequence phylogeny.

Language: Python - Size: 1.28 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 2

mbbu/16S-mini-project

This is a workflow for 16S rRNA analysis.

Language: Shell - Size: 60.1 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 6

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 at: about 2 years ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 2

GuilleGorines/16S-Qiime-protocol

16S procedure using Qiime2

Language: Python - Size: 220 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1

BryanAbuchery/16S-rRNA-End-to-End-Analysis

Qiime2 and DADA2 are one of the latest bioinformatics tools used in 16S RNA analysis. The current Qiime2 and DADA2 pipelines support End to End 16S RNA analysis, among other analyses.

Language: Shell - Size: 2.76 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 3

bioinfonupeb/microbiota_da_mulher_lbbm

Projeto de análise metagenômica e metabolômica da microbiota de mulheres no climatério - LBBM UFOP

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rjstevick/AllNBayWildOystersCombined

Scripts for combined 16S analysis and Rscripts to make figures for conclusions chapter of dissertation

Language: R - Size: 4.73 MB - Last synced at: almost 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0