cafferychen777/MicrobiomeStat

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

Language: R - Size: 15.7 MB - Last synced: about 12 hours ago - Pushed: 1 day ago - Stars: 24 - Forks: 3

noriakis/q2-pathway

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

Language: Python - Size: 158 KB - Last synced: 4 days ago - Pushed: 5 days 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: 5 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0

nf-core/ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Language: Nextflow - Size: 14.9 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 157 - Forks: 105

micom-dev/q2-micom

A Qiime plugin for MICOM.

Language: Python - Size: 65.3 MB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 10 - Forks: 3

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: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

biocore/empress

A fast and scalable phylogenetic tree viewer for microbiome data analysis

Language: JavaScript - Size: 45.8 MB - Last synced: 1 day ago - Pushed: almost 2 years ago - Stars: 45 - Forks: 31

ohmeta/qiimepi

Snakemake version of QIIME2

Language: Python - Size: 163 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

segrelab/MiCoNE-pipeline-paper

The source code for the MIND pipeline paper

Language: HTML - Size: 61.2 MB - Last synced: about 2 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

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: 122 MB - Last synced: 27 days ago - Pushed: 4 months ago - Stars: 63 - Forks: 17

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: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

sbslee/dokdo

A Python package for microbiome sequencing analysis with QIIME 2

Language: Python - Size: 11.9 MB - Last synced: 15 days ago - Pushed: 4 months ago - Stars: 41 - Forks: 12

Gibbons-Lab/isb_course_2023

Materials and presentation for the 2023 ISB Microbiome course.

Language: Jupyter Notebook - Size: 245 MB - Last synced: 4 months ago - Pushed: 4 months 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: 4 months ago - Pushed: 4 months ago - Stars: 10 - Forks: 2

StephRut/MSI-QIIME2-Pipeline-Tutorial

Language: HTML - Size: 232 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

DavideScarpetta/taxonomic_profiling

Metabarcoding analysis pipeline, using DADA2 and qiime2

Language: Shell - Size: 65.4 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

Gibbons-Lab/isb_course_2022

Materials and presentation for the 2022 ISB Microbiome course.

Language: Jupyter Notebook - Size: 258 MB - Last synced: 4 months ago - Pushed: 7 months ago - Stars: 23 - Forks: 8

yjiakang/amplicon

amplicon pipeline

Language: Shell - Size: 5.13 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 0

focussash/MiCoMo-Manuscript

Files for the MiCoMo project and manuscript

Language: C++ - Size: 2.54 MB - Last synced: about 2 months ago - Pushed: 7 months 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: 7 months ago - Pushed: 7 months 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: 8 months ago - Pushed: 8 months 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: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 1

PlantGGHLab/qiime2-nf

Microbiome analysis with QIIME2

Language: Nextflow - Size: 1.48 MB - Last synced: 9 months ago - Pushed: over 4 years ago - Stars: 3 - Forks: 0

HSapers/q2-decontam

qiime2 decontam plugin

Language: Python - Size: 1.87 MB - Last synced: 9 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 3

rjstevick/loperamide-zebrafish-dysbiosis

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

Language: HTML - Size: 113 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

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: 10 months ago - Pushed: about 1 year 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.

Language: HTML - Size: 31 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

sPuntinG/Galaxea_Microbiome_PCI

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

Language: R - Size: 11.9 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

SharuPaul/Metagenomics

Data analysis using QIIME2

Size: 78.4 MB - Last synced: 7 months ago - Pushed: about 1 year 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: 11 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 1

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

Zubair2021/16S_Microbiome_Analysis

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

Language: Shell - Size: 33.2 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 1

rjstevick/zebrafish-conv-mix9-models

Analysis of 16S rRNA and microscopy data from larval zebrafish

Language: HTML - Size: 188 MB - Last synced: 11 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

telatin/qax

Qiime2 Artifact eXtractor

Language: Nim - Size: 15.3 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 4 - Forks: 2

leylabmpi/qiime_2_ll_quick_viewer

Language: Python - Size: 72.3 KB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 3 - Forks: 2

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: 6 months ago - Pushed: 6 months 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: 3 months ago - Pushed: 3 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: 187 MB - Last synced: 3 months ago - Pushed: 3 months 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: about 1 year ago - Pushed: almost 2 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: about 1 year ago - Pushed: over 2 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: about 1 year ago - Pushed: over 3 years ago - Stars: 5 - Forks: 2

gibsramen/evident_

Effect size calculations for microbiome data

Language: Python - Size: 1.38 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 4 - Forks: 1

GuilleGorines/16S-Qiime-protocol

16S procedure using Qiime2

Language: Python - Size: 220 KB - Last synced: about 1 year ago - Pushed: over 1 year 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: about 1 year ago - Pushed: over 3 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

Language: HTML - Size: 63.1 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

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: 11 months ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0